I stopped keeping variations in one plan, for several reasons. I do a lot of material takeoffs, and sell cad files, both get extremely complicated if combined with variations. Also just the inherent weakness and propensity for human errors when handling variations with layering. The downside is realizing you had an error on the base plan so you have to open the following plans to correct, but that should be minor.. in theory:)
I do my detail numbering a bit unorthodox, but it works well enough for me (and a University of Fl professor used it as an example of good organization in a book he published.. so I feel justified:) Having all you details in one pln works for me in that I can handle variations extremely well with layering. I do stock plans, so I need easy access to variations. I can have a basic eave detail with layering turning on and off different pitches, exposed tails, boxed etc. That makes it easy to add variations. But that's my internal file so it doesn't confuse anyone else. I number them sorta logically, F1, F2, F3 etc for foundation.. and keep those details on the foundation sheet, not at the end of the drawing set which is more trouble for someone reading the plans flipping through pages to get a detail, even with page number referencing. It simplifies my work and the person reading the plan. I keep eave details by the building section(s).. etc. My sets are small however (10 sheets or less) .. not large commercial projects.
That screen shot is unique to AC10, that's why I posted it. From within 10 you are connected to other plns. Here I have the detail pln displayed while in another plan file. You simply drop the details onto the sheet. The same thing applies to lbks, but you are dropping them into the book from Finder (or whatever windows does). The details are simply organized by .. I'll just add a collapsed tree screen shot. In this screen shot I have a porch column. With layering I can turn parts on and off making different columns relatively easy, and saving the view. Having them all in one file makes placing them quicker and easier. (thanks to Erika for that inspiration:)