Once you have Clockwork it is there it does not get replaced until you replace it / put the SBF back on there.
As for flashing from the SD Card, you *can* do that, but if you have ROM manager premium, then you can use *it* to flash for you.
If you opt for manually flashing, be sure to make note of which recovery you need installed in order to flash a particular ROM. A lot of them use CWM but some still use SPR, so read carefully before going crazy - and always, ALWAYS ALWAYS make a manual back first before doing anything, just in case you do skip the need for a required recovery and format ... and have a useless phone.