The purpose of a jointer is specifically to flatten warped lumber. If your lumber isn't warped, you don't have to joint it. In a fantasy world, none of us would need jointers. Unfortunately, in our world wood moves, so even if the lumber was jointed perfectly flat before you bought it, it probably won't be perfectly flat by the time you go to use it. Certain species and certain cuts will be more susceptible to warping.
Let's assume your jointer is properly-tuned. In other words, the top surface of the outfeed table is perfectly even with highest point of knives as they rotate, and the top surface of the infeed table is perfectly parallel to the top surface of the outfeed table--i.e., the infeed and outfeed tables are perfectly coplanar when raised to the same height, even with the top of the cutterhead's arc.
Now we're ready to start squaring up a board.
First, you joint the face, taking one or more shallow passes at a time until the face is flat. For this pass, you hold your workpiece against the horizontal infeed and outfeed tables. Depending on the size of your jointer, most consumer-grade machines can safely remove up to 1/32" or 1/16" per pass. Once you think the piece is flat, you can prove it's flat by scribling with a pencil across the entire face and taking one more shallow pass. If all the pencil marks are gone, your workpiece is flat.
Now that you have a flat face, you joint one edge. Set your fence exactly 90 degrees to the tables, then hold the newly-flattened face up against the fence. Pass the workpiece through the jointer one or more times until the edge is perfectly flat, again taking shallow bites.
That's it; assuming you have any wood left, you're done and you can move onto steps 3 and 4, ripping the other edge parallel to the first (usually with a table saw), and planing the other face parallel to the first (usually with a thickness planer).
But what if you don't have any wood left? In that case, you're probably sitting in the emergency room waiting to have your injuries treated, which means you should have done something differently. Let's hop in our time machine and do it right.
Deal with severely warped and/or long boards before they even touch your jointer
As I mentioned in a comment, sometimes you simply cannot remove all the warp with only a jointer, or if you did you'd have little or nothing left to work with after jointing. For this, you'll need to do some crosscutting and/or ripping (or karate-chopping), which you can't do with a jointer.
The longer, wider, and thicker your lumber is, the more likely it is that there is some noticeable warp, whether it's a cup, twist, bow, crook, etc. But the warp may be more pronounced in one particular area. In the most severe case, if you take a severely warped board and choose any points, one on each end of the board, there may be no straight path from point A to point B which passes only through wood without passing through air. But if you crosscut the board in half, you will usually find that it's much easier to find a path from point A to point B without passing through air.
So before you ever start dimensioning, you should cut the piece down to rough oversize length. Crosscut each piece a couple inches longer than your final dimensions (or maybe even longer, if you have to account for joinery or some extra fudge factor), but keep each piece at least 18-24" long if you plan on jointing. Now that you don't have to remove most of the wood in order to get a flat board, you can start jointing to remove each type of warp.
For a crook or kink, you should flatten a face first so you can register it against the jointer's fence. After that, the steps are basically the same for a bow, crook, or kink.
Method 1: Place the concave face (for a bow) or edge (crook/kink) down so both ends are making contact with the infeed table. If your infeed table is not long enough to support both ends of the board, you can add an extension or auxiliary infeed table.
Method 2: If the crook/kink is severe, you can start by making a few shallow passes with one end on the outfeed table and one on the infeed table, then finish with method 1.
Twist is the most difficult type of warp to deal with, and is easiest to tackle with a planer sled. But you can do it with a jointer with a little bit of finesse.
To preserve the most thickness, you want to start out by removing equal parts from each end of the twisted board.
For shorter pieces, you can hold down one edge of the piece on the infeed table, but for longer pieces you have to balance the twisted board freehand for the first several passes. Matthias Wandel has a nice article illustrating this technique.
You can't fix a cup with any amount of crosscutting. If you have a severe cup, jointing and planing away the convex belly on one side and the concave cup on the other side may leave you with little or no thickness left. What started out as an 8/4 board may now only be 1/2" thick. A better solution may be to rip the board narrower. The narrower the board, the less severe the cup. So you could rip the board into strips and, depending on your needs, either joint each one individually before gluing them back together, or you could preserve a little more of the board's width (probably at the expense of matching grain patterns) by flipping every other one over and gluing them back together.
But let's suppose the cup is shallow enough to joint. If your jointer is wider than the board, joint with the concave side down. If your board is wider than your jointer, joint with the convex (belly) side down.