for that you can use SolidWorks Explorer or Pack'n'Go to rename your files and maintain/update references appropriately. This really depends on how many files you need to update as to what I would pick... but about the best sure fire method is to open each sub assembly on it's own and do a pack'n'go to update to all new names. then move forward with all unique names to put into your top level assembly.
the preventative measure in the future is to not duplicate file names anywhere.
Thanks, Paul, Pack'n'Go saved me a lot of time. As for file naming in the future, solidworks was automatically generating names (1,2, etc.). On my most recent import, I selected "import multiple bodies as parts" and it seems to have retained the original part names the author used which solved my problem.