Multiple Companies on same instance - managing government reporting

I am currently at a client site where there are 4 distinct companies running E1 on the same instance.  Each company processes its own SUI reports/files and W2 reports/file.    This is a challenge to manage, as electronic files are named the same for all companies/year end IDs,  and overwrite each other if we're not carefully managing the process.

How do other  companies handle this?  What's the best practice?  Any advice?  Are there any enhancement requests for renaming the flat files, appending them with the Year End ID, or company #?