I've flashed Clockworkmod recovery from within Rom Manager twice before trying to flash the rom.
Update: When I flashed it again it apparently "took" this time. All seems to be going well!!
Thanks JkdJedi
Until you delete the file "recovery-from-boot.p" from /system your custom recovery won't stick (you won't have this problem when you flash a custom ROM as they all have this taken care of already, so you can wait until then)
OK...I tried flashing JBS 3.1 and it aborted the install so I tried flashing JBS 2.2 and it aborted. Then I tried CNA 3.8 and it aborted. I'm pulling my hair out!!! I restored original stock rom but woulsd like to proceed. What am i doing wrong? I'm running 4.1.1
Firstly I wouldn't recommend either of those ROMs, I suggest AOKP or CM10 (since you seem to be looking for something with some healthy options, based on your choices). Secondly make sure before flashing you are wiping everything within recovery. Don't use ROM Manager to flash. Use it to flash and boot into your recovery (if you must, lol), then from within recovery:
Wipe data/factory reset
Wipe cache
Wipe dalvik cache
Wipe system (Format /system under Mounts & Storage if using CWM)
Then flash the ROM and gapps and reboot. Double check that you are downloading the correct ROMs for your device as well.. VZW gnex is Toro, it should say this in the ROM description or filename.