OK, here is what I do to not have a duplicate file:
1) Both my cameras have different prefixes set up, DRB and DB2.
2) I let LR do the import from my camera card to do steps 3 and 4 for me (you can batch rename files but LR seems to do this just fine).
3) LR adds a custom name on import, yyyymmdd{filename} (as the RAW files have a filename that starts with an underline "_" a sample filename after import is: 20151031_DRB5830.NEF and that ensures that no two of my filenames will ever be the same.
4) LR automatically puts my RAW files into a new directory that is called yyyymmdd and that goes into a Year subfolder.
5) That it. Basically if I do ever mess things up (and I have) the file name and the folder have the same name so I can get things back in order very quickly.