I know almost nothing about robotics, so I was wondering how can I power the nxt motor without using the nxt brick, and how can I send signals to it?
I think the simplest way is to use an NXT Converter Cable (Available from Bricklink). This has an NXT connector on one end and the standard 9v connector on the other. You can connect the 9v connector to any 9v battery box, (e.g. Battery Box with Switch (9V)) and, depending on the polarity, power the NXT motor forward or backward.
Now, the issues: