As I understand it, ACAD will read through the contents of all of the folders defined in the "support file search path" section of the profile, and run the first acad.lsp and acaddoc.lsp it finds. My mistake was that in testing various configurations, I had multiple profiles, and in one of them for some reason (I've forgotten what it was) I had added my desktop to the search paths.
So, yes, I think you can have multiple acad.lsp's and run the correct one simply by controlling the order of your search paths. But I think a better solution would be to only have one acad.lps in your search path anywhere, and if you have draft copies, or different acad.lsp files for different profiles, put the in folders that are outside the search paths.