When I download and install a rom, the file normally already has its own name. I can see where changing the name might affect the MD5 number but it should still install ok. You might get more opinions though.
You can rename them if you want to. I have found if you just do a nandroid through ROM Manager though it is easiest to just rename it when it prompts you to. Your choice I have renamed them both ways and been fine.
When I try a ROM I install it and delete the zip file after the install. I then get it set up the way I want it and do a save through ROM Manager to whatever I feel will make me remember it. You do not have to keep any of the name that ROM Manager recommends. Then I move on to my next ROM and do the same.
This way, if I want to go back to a ROM I just restore it with ROM Manager and it is also already set up.
You can rename a ROM before but it may fail the MD5 check.
You can rename a backup but after it is made but it may fail the MD5 check. In this case just add something at the end of the backup folder name that you can remove later if it gives you a problem.