Planning ahead and asking

Planning ahead and asking questions is highly recommended. Visiting other multi-deck layouts will give a better sense of reality. A flooded basement (future layout room) will provide years of frustration and disappointment. I will assume this will be addressed before construction begins.

What is the purpose of each deck? Staging, yard, industrial switching, scenic run though? All have different requirements.

What is the separation height between each level? 

What is the plan to travel between each level? Helix, Nolix, transfer table?

Generally, from what I have seen others do, deck depth decreases on the upper decks. This help avoid ducking under a higher but deeper deck to get to "stuff", and accidently bumping into other "stuff".

Keep us posted.

Wazzzy

Depends...

Generally yeah, more narrow up top than down below, but it depends on a the height of your decks and the separation between decks.  Make a mock-up out of cardboard or something and stand where you'll stand when operating and check your height and depth that way.  Remember to mock-up the thickness of your decks too. I set my heights so that I could see all of the middle deck, from fascia to backdrop without stooping.  You don't even really notice the upper deck that way.  I used steel benchwork so I could keep the decks as thin as possible.  The upper deck is often just as deep as the deck below, and occasionally even deeper, but it works. 

Randy 

Room preparation

The room will be well prepared - the plumber was here today. He will close a sewer and will install two stop valves - so I should be safe in the future.

Shelf Brackets

I suggest getting a couple of those slotted channel shelf supports and some long and medium shelf brackets.

Then put some boards/foam planks/shelving/cardboard on the brackets and test various heights and depths.  Cut some strips of cardboard or poster board the width of you deck thickness and attach them to the front of your shelves to see what the viewing angles are.  It will probably cost less than $20  but will give you all sorts of insight into your design.

get tony koester's book

Designing & Building Multi-Deck Model Railroads

many practical suggestions

Good comments so far. I will

Good comments so far. I will add how wide are your aisles are they wide enough for a seated operator and a standing operator? What are you modeling? The subject matter makes a difference on depth and space between levels. 
For example relatively flat midwestern terrain will not need near as much depth or height as models of steel mills or other very large industrial items in an urban environment. A large yard might need lots of depth but not lots of height if you’re not including a coal tower.

I am planning a layout with 4 different levels. Two staging and two for operation. I will put the staging at the top two levels with a foot between them. The top operations level will be 56 inches high. The decks will be 4 inches or less in thickness. And there will be 22 inches between the top and bottom level. The lower level will be 30 inches above the floor and be operated while seated. The top level will need to have the same 22 inch minimum between it and the first staging level.

Now those dimensions will work for me and what I want to model but might be of no use to you. I suspect you will need to consider what you wish to have and come up with your own space. Some of the books mentioned in discussions like this often recommend 16 inches between levels but that would not work for the area and things I want to model.

My Experience

I found the Tony Koester book mentioned in an earlier post invaluable when I built my first multi-level layout.  Read it and digest it's material.  It will help immensely.

As for my own experience, on my previous layout, the Pokey 2.0, I limited the upper deck width to 16" on most of the layout.  The lower deck width was limited to 30" width, with 16" inches of vertical separation between the decks.  

On my current layout, the Pokey 3.0, which is still under construction, I tried to limit the width of the upper deck to about 16" as well.  However, at the end of the peninsulas where the track makes a 180+ degree turn, the upper deck width ends up being the same as the main deck.  Not ideal, but I increased the deck separation somewhat to compensate and provide more visibility for the main deck. That being said, the closer the deck is to eye level, the less deck separation is needed for good visibility. 

A picture is worth a thousand words they say, so here's a diagram I made for myself with the XTrackCAD program I used to design my layout.  (Right click on picture and open in new browser window for larger view.)

These dimensions work well for my height, which is 5'6" (the shorter stick figure).   Most of my railroad friends are taller than I am, more around the 6' mark, give or take.  These dimensions might not be ideal for them, but none of them complained when running op session on the Pokey 2.0, and when asked about it, replied the deck heights were very reasonable and workable for them. 

Hope that helps a bit as you make plans for your layout.

minimums

For the helix  :

There's an NMRA standard for that. its roughly around 3 inches separation from railhead to bottom of the sub bed , To maintain that separation with a reasonable 1.5% grade , your looking at around 36 inch radius with 1/8 to 1/4 sub bed and no roadbed.

You can get away with going under the standard clearance , down to 2 3/4 ish with 1.5% thats about 30 inch radius .

You can increase the grade to 2% and maybe get down to around 26 inch radius.

As you go under 3 inch clearance , some cars will not be able to make it thru the helix ( cranes) , under 2 3/4-2 5/8 Hi Cubes and Amtrak Highliners start to hang . 

To calculate the grade you use the rail head to rail head distance (the vertical distance the train has to climb NOT the clearance distance)

For the decks :

Top scenery deck will chest high or slightly higher ; bottom deck  18 - 30 inches lower.  For appearance , lighting, and access reasons   its usually best to set the top deck back 6 -10 inches. 

for staging areas on the bottom ,don't set them back , it makes it a nightmare to get access. bring them out flush with the lower scenic deck , you can always cover it with curtains. Ideally you want to be able to sit on a stool or box and see what you doing.

Cardboard Mockup & Paper Templates

Here is what I did to get some ideas for my multideck layout I was planning for my hand-house shed. I went to a few furniture stores to get big pieces of cardboard to cut up for my decks.

https://forum.mrhmag.com/post/help-please-design-a-dbldeck-layout-in-its-own-handhouse-shed-12207028

https://forum.mrhmag.com/post/help-please-design-a-dbldeck-layout-in-its-own-handhouse-shed-12207028

I ended up changing my track plan eventually, but by then I had me deck height spacing worked out. I could even draw pencil track lines on the cardboard.

Perhaps you will be using some computer program for planning out your track plan,....but just in case you choose to draw it out, here is what I did with a roll of brown paper,...full size track planning.

Full Size Paper Templates of Trackplan
https://forum.mrhmag.com/post/full-size-paper-templates-of-trackplan-12211674

Better get that water problem completey solved first.

This idea is not mine but was

This idea is not mine but was done by another model railroader. He placed models on adjustable bookcase shelves to see how he liked the spacing. Keep in mind you will need space for your tallest structure or scenic elements. If 16 inches works visually you still will not be able to put a blast furnace or basic oxygen furnace in there. Same if you are putting in a city scape with tall buildings 

I'm a fan of the mushroom

I'm a fan of the mushroom multi-level concept, as opposed to the traditional approach. Something worth looking intonif you're not familiar with it. Cross-section  here