Helicon Focus and focusing...
Rick,
You're succumbing to FUD (fear, uncertainty, and doubt). Don't do it.
First: focus stacking programs like helicon focus need an image stack that are all the same white balance and exposure. This precludes using ANY kind of automatic white balance, auto ISO selection, or exposure control (such as aperture priority or exposure priority).
Why?
Because as you focus back an forth in the image you're also zooming slightly. As you zoom light and dark portions of the scene may get "zoomed" out of the image causing an auto exposure mode to mistakenly change the light sensitivity making some of the images in your focus stack lighter or darker. The same applies to brightly color objects getting "zoomed" out of the picture causing the camera to rethink its automatic white balance.
You want a camera that offers MANUAL control over everything. Then set it to full manual control, determine a good IOS, white balance, exposure time, and aperture and use them for ALL the shots in a focus stack (set of pictures each of which is focused slightly differently).
Manual focusing is workable. I shoot a LOT of focus bracketed shots for MRH that I process with Helicon Focus. I can't remember the last time I used the remote control software for my cameras for this purpose.
You WILL need to hold the camera steady. A tripod is the best way to do this. But just plopping the camera down on a flat spot on the layout works. Event setting the camera on the rails works (but put a piece of paper under it to avoid shorting out the rails and having the DCC booster weld the camera to the track -- I'm serious about the paper, but not about the welding which ain't gonna happen). If the camera is just set on the layout you'll need to be very steady in holding the camera in place. Think I'm kidding? Nope -- I shoot a lot of focus stack photos with the camera sitting on the track.
The key to shooting focus stacks with a moderately precariously perched camera is the ability to focus smoothly and effortlessly. By that I mean the best way to focus is with a smooth-turning focus ring on the lens. If the focus ring is stiff you'll need to apply too much torque are and likely to "jiggle" the camera between shots. If that happens don't sweat it, delete what ever photos you've already shot for this focus stack and try again. I've been know to try 3 or 4 times to do a focus stack when the camera is awkwardly placed for me to hold. Just think of Horace Fithers using one hand to firmly press the camera down on where ever it's sitting (like some rails) and the other hand to alternative "tweak" the focus and press the shutter.
When placing the camera on top of the railroad, DO be very careful where the strap sits. Don't let it foul delicate details. Don't let it hang over the edge of the layout where you can snag the strap when you walk by or you will be buying a new camera when the old one becomes intimate with your concrete floor.
Cameras without a focus ring are going to be no fun at all. Using a menu to focus involves far too many intricate motions around the back of the camera to be able to hold it still. You can probably do this with a solid tripod, but it will be painful getting each focus step right. And it's just plain ain't gonna work if you're setting the camera on the layout. This is a place where remote control focusing (and shutter release) software would help (a LOT).
A camera with an articulated view screen on the back and live view capability (the ability to continuously display on the view screen what the photo would be if the shutter is pressed) is handy. Twisting the view screen around makes it easier to see what's on it without putting a crick in your neck from the contortions necessary to get an eye-ball into good position. But, articulated view screens tend to be smaller and lower res than fixed displays.
One more thing about focusing -- focus stack software such as Helicon Focus like to have relatively even focus distance steps between the individual images. When I'm shooting a focus stack, I try to turn the focus ring the same angular distance for each successive photo. Looking at the bumps on the focus ring can help keep those distance consistent. They don't have to be perfectly consist, but evenness is better than unevenness.
Almost any kind of DSLR is good for focus stacks. Compact point and shoots just plain won't work. Pro-sumer grade compact cameras with full manual control may work well depending on how focusing is controlled. A prosumer compact camera will probably have a remote control interface. But such a camera will likely cost as much as the less expensive DSLR cameras.
If you end up camera shopping look for one with a macro lens that will let you focus as close as about 10" away. The lens should ideally stop down to f/32 (for a DSLR) though f/22 is OK. I typically use f/16 for focus stacks with my 17-50mm Tamron macro zoom. When shooting focus stacks with my 100-300 tele-zoom I usuually go for f/22 or f/32 so each component shot will have some depth of field of it's own (which makes life easier for Helicon Focus). Compact prosumer cameras typically have a much shorter focal length lens and will give good depth of field at f/8.
For more on "layout photography according to Charlie (and Horace)" you might check out the pdf file of my Model Railroading Clinic from the Sacramento National Convention in the bonus extras for the August 2011 MRH.
Hope this is helpful.
Charlie