Ray's advise is solid, like always. The status calc (or Get function in v7) is very useful. FileMaker 4/5/6 will keep track of every path the file has been located, so even it you move it FileMaker will still look for the file in that path if it can not find a file.
When using older versions of FileMaker, I will compress my old files into an archive, because more than once I will find that my solution is using files that are in different folders. FMP 7 let's the developer see these File References, but without third party tools FMP6 whould not let you access the 'list of know paths' for a specific file, so the next best thing is to check the path with the (CurrentFilePath) function.
A step further would to have you startup script to open all the files in the solution and make sure that all you paths have the same root. i'm thinking of something like Left(Status(CurrentPath), Position ("/",1,-1)).
Hope this helps,
Joe