So, probably a proper noob question, but if I hit someone in their flank, can they hit back? If so, which models make the attacks?
They can hit back, but only the models that are in base to base. There are no supporting attacks when you are attacking to the flank. Also, you don't get parry saves from attacks on your flank.
Also remember the Combat Reform. If the flanked unit is lucky enough to stick around after a beating, it can turn to face the immediate threat.
The winning unit in a combat can reform after combat, but the losing unit must make a Ld test with a penalty equal to the penalty they took their break test on.