If you flash a newer version it will just replace the old one. Flashing TWRP will also replace CWM so you will only have one recovery. Using older recoveries and flashing newer roms, like Jellybean, can sometimes cause bootloops. The newer recoveries do a better job of wiping. I don't know about CWM, but using TWRP, I can auto-update the CM 10.1 nightly rom builds and TWRP will automatically wipe the caches and install the rom.