There needs to be a hard and fast methodology to how these files are created and saved. I read on here one time that somebody alway uses the pre-cursor, "CUTFILE_filenameblahblah.ai" to distinguish it from the others. I've since used that and it does save time.
There's those few things that need to be remembered at the end, depending on what you're going to do with the file. In Illy, when using the pathfinder tools, I've noticed duplicated paths that have no fill or stroke, so the last thing I do before I cut is draw a line that has no fill or stroke, then "Select>Same>Fill&Stroke" to get rid of them.
Maybe this thread will generate some input as to how others approach this. I've done the multiple layer thing and it's a great idea, it's just remembering to do it, especially when the purpose of the file is to be cut.
Ctrl-Shift-O She's a pain sometimes!