I use a Recording Buss
Well I have all tracks going through a "BUSS" then to the Master track.
You can record on that track as you play Reaper.
I use the buss loaded with ReaInsert to use my Hardware compressor and EQ.
After recording it is wise to shift the file along the time line to avoid
playing back that file and the rest of the normal tracks together.
However you can shift the recorded file to another single track with it's output to "Master Track" and solo it before you Render or other wise just mute the Buss track and render your file with ease from the custom audio track as long as all the normal tracks to your musical creation point to the BUSS and only the BUSS.
I think that makes sense...
Grinder