Mark I'll try to ease your mind
When your Jig arrives the PC board ties will fit the jig width wise you will need to cut them to length then using a 1 inch wide fine 10 mil. single or double cut file you will need to lightly file each PC Tie on all four edges just before dropping them into place on the soldering and layout turnout jig.
You don't need to worry about the wood ties until the solder work is finished. When I lay the wood ties out I align them so that the are even on the straight side of the turnout and glue them down to the turnout turned upside down.
After the glue dries (the next day) I lay the turnouts on the table rail side up and check all the switch points to make sure they move freely and then with a new SHARP X-acto Blade or a new Sharp single edge razor and carefully trim the ties on the curved side of the turnout.
ATLAS vs Micro Engineering (ME) Track:
Not to worry you can use your Atlas flex track or any flex track with your ME rail equipped turnouts no trouble as the bottom of the Atlas rail is wider the Top should line up perfect.
Should the Atlas be slightly wider on the inside top edges of your rails take a 6 inch long - fine cut Jewelers file and lightly file the wider section on the inside of the two rails, about two or three passes should do the trick.
Stock Aid Tool:
I have built a little more than 100 fast tracks Turnouts and have never used the stock aid tool. What I use is a Jewelers Grinder, I'm sure the stock aid would have made the job easier. The main reason I didn't use one is that "FAST TRACKS" didn't develop it until after I had built all the turnouts. Basically its up to you, If your real good with your hands and have excellent dexterity you won't need one if your just starting to use small tooling I would suggest you get one.
Tools you really should have and should be able to get at the neighbor hood Hobby Shop at a lower price than Fast tracks sells as there is no shipping charge
1; Xuron Track cutting tool - will cut rail flush and square (a Must)
2: Jewelers Saw - with fine tooth blades, Buy a 5 pack of fine or extra fine saw blades they break easy.
3; 10 mil Fine single or double cut File they are 1 inch wide and 10 -12 inches long and get a file handle to make life safer and easier to handle the file. (a must)
Don't use an old 10 mil file buy a new one and use it only for building Fast Tracks turnouts ONLY
4; 25 watt pencil type soldering Iron Avoid the junk Radio Shack sells find a Weller Soldering iron their about $20-25.00 or Weller soldering station $90.00 - $125.00 the 25 dollar unit works fine
5; Buy a bundle or two of rail you'll use it up fast and buy extra PC board ties and a few bags of wooden ties or if you prefer buy the Twist Tie Kits they make 6 turnouts per kit
6: Don't forget to buy the Pliobond contact glue. Fast tracks sell it for $5.59 for 1 tube or if you have an ACE Hardware Store near you they sell it for $3.70 a tube and $6.25 for a 3.5 ounce bottle. I use a syringe with the larger bottle as an apply tool.
You asked"how long does it take to build a turnout?"
your first 1-2 hours as you watch the videos as you build.
take your time when building your first few turnouts and follow the instructions one step at a time in order to make a quality turnout right from the start Just don't rush.
Later when you get the hang of it you can make 2 turnouts per hour with no trouble but the first one may take more than an hour to construct. Remember it's not a race so work at what ever pace suits you.
Good luck take your time and Happy Railroading.
Dan