You can use the Developer Tools on a subfolder set of files before uploading to Rename the Files, then upload the renamed files:
Server / ClientA_Solution.fmp12
Server / ClientA_Data.fmp12
Server / ClientB_Solution.fmp12
If you name the files appropriately to the client and set each file to display in the server only if the user has an account in the file (cleaning out accounts not intended for each client) they will each see only their own specially-named files.
P.S. Developer Tool for renaming is available only in FileMaker Pro Advanced, and it takes care of updating file references within the file group selected.