Well, we all do different things, and some of us for the same reasons, but to put it bluntly, you pour the beer into the secondary so it can clarify.
Doing this also takes the new beer off of the old yeast (lots of debates about the why's and such - in this case just take my word on it) and allows the beer to finish fermenting if it is not down to the FG for the style.
It should remain in the secondary for a week or so. You can check the gravity after a week or so if you wish.
When the FG comes within the desired range for the style it is ready to transfer again into a bottling bucket.
If you have a full 5 gals then you should prime the brew with either 3/4 C corn sugar or up to 1/4 C Dry Malt Extract (DME).
Bottle and wait....you can read other threads on what to do next.
Also note, you don't want to just pour the beer from the primary to the secondary, you want to rack or siphon it... and you want to avoid splashing, sloshing or any other agitation that would cause oxygen or air to get into your beer. Aeriating your beer at this point will cause off flavours.
I usually leave my beers in the primary for a week. Sometimes I've left them in the primary for two weeks. My beers usually get two weeks in the secondary fermenter and they are pretty dad-gum clear.