I've often found it is easier to keep stuff heavily separated out so you can tweak or re-purpose bits. My typical PSD layouts are more like material compositing and less like painting, they might look something like this (these names are layer groups, with a layer mask on each group):diffuse dirt mud moist dry soot decals…
Interesting - I mean, all of our PSDs are in the same heirarchy and grouped the same. So one thing we could do is include all different variations in groups (dirty, clean, painted, for example) and allow the user to just mask between layers they like and don't like. Then it would just be a matter of saving out of photoshop…
Rome wasn't built in a day Seaseme, and I think it's impossible to know what is right until you've got it wrong. I'd just spend 5 minutes going through a few PSD's each, maybe have a round of comments if anyone has some major issues with anything, then put them up for download with a clear 'comments' section on the page…