As was mentioned before, you give positive/negative rep by clicking the little blue box down and to the left of someone's name beside their post. You give positive rep by saying "I approve", and negative rep by saying "I disapprove".
To check your rep, go to User CP in the upper left, and then go down to the words User Control Panel (which look like a red heading, but is clickable). Your last five items of rep will show up there (you may also get a PM whenever someone gives you rep).
Green is positive and given by people with a positive rep. Blue/gray can be either negative or positive, but doesn't change your rep level, because it's given by someone who doesn't have any points yet (hence, the system doesn't see them as able to affect others' rep - either because they haven't posted or gotten rep). Red is negative rep, which brings your total rep down. Somebody either didn't like what you had to say or the way you said it (or they're just being disagreeable).