You can usually adjust the levels on two channels, so a 2 channel amp would have one lot of equaliser setting, a 4 channel would have two sets, a 6 channel 3 etc.
The front components would be controlled off the head unit. You can then set the amp to control certain frequencies, i.e the 6x9's would be allowed to play anything at around 80Hz, on the first two channels.
You would then probably bridge the sub on the next 2 channels, and set it to play lower frequencies.
Although ideally you'd have a seperate amp for the sub.
EDIT: That was a bit of a crappy explanation. In answer to your question, an amp would almost certinally help.