Top-down incremental compilation

You can have your files wherever you want. Project -> Add Files let's you point to them. Also note that you can use exact paths or relative paths, whatever your preference is.

How long are your compile times? To be honest, I really don't see any need for incremental compilation. You should easily be meeting timing, so it has nothing to do with preserving performance. If you try a Fast Fit(Assignments -> Settings -> Fitter -> Fast Fit) you should get a very fast fit. Let me know how long the compiles are. Note that there's a point where the savings probably don't justify any additional work, i.e. if you've got a 25 minute fit time, and incremental compilation saves 5-10 minutes per compile, but you spend time creating floorplans or anything like that, then it's probably not worth it. (But if you do want to pursue, hopefully I answered that you can have your files in multiple directories for the top-down approach.)