Hee's what I do.
Create a separate directory for each project. Like
D:\Reaper Files\Song #1\Take1.rpp
D:\Reaper Files\Song #2\Take1.rpp
D:\Reaper Files\Song #2\Take2.rpp
D:\Reaper Files\Song #2\Final.rpp
etc.
Somewhere there is an option to save the Media files in the project directory. I'm not at my Reaper PC right now, but if you can't find it someone else will probably have the answer right away. Or check the user guide (
https://www.reaper.fm/userguide/Reap...Guide5961d.pdf) -- it's in there somewhere.
Also, try not to use generic file names (if you are). There is an option to add a timestamp to the files, so that "vocals.wav" gets unique-ified by the exact date/time you recorded it. (Again, not at my Reaper PC, but it's in the manual I think.) I use that option, and it certainly helps me keep track of which file I am using.
I use all three of those techniques, and find it is pretty easy to keep track of the files (as long as I use better directory names than "Song #1", "Song #2", !!!)
The basic idea is that the media files (MIDI, WAV, etc.) reside in the project directory, so are always easy to find. And each "Song" has a separate directory, so that the number of files in the project directory doesn't become overwhelming.