Think of the jointer as just a big hand plane, and don't expect it to solve a problem in one pass. Think about where you would have to remove wood to get the board flat, if you were planing it by hand. If it's concave, with a hollow in the middle, then it would be on the ends. If it's convex, like a saucer on the table, then the middle needs to go away. In your case you have to rest the far end of the board on the outfeed table and slowly lower the middle onto the cutter head as many times as is necessary to remove the belly, or convex area. Just be carfeul and watch were you hands and fingers are. You must also not try to joint a board that's too short, less than 24", starting out. Any thing shorter than that is asking for trouble.
Now, my next question is do you have a thickness planer? You really need both to mill and surface rough lumber. Lumber will bow and cup as it dries, slightly or greatly depending on the grain direction and moisture content. Once you get one side flat on the jointer, the next step is to thickness plane the top side down to the dimension you need for your project, let's say 3/4". That's why rough sawn lumber is generally 1/4" thicker before you start surfacing it, say 1", to allow for enough wood to be removed to get the surfaces flat and true. I hope this is helpful to you,
I just found an old post on this subject from 2-09:
Visually sight the board first. Does it have a warp, twist or cup? Or all 3? There is nothing that says you must joint the entire length of the board in one long pass. In the case of a warp, place the convex side down and joint each end in a little ways in by flipping the board end for end while staying on the same face, until the board becomes "flat" then joint all the way thru on the last several passes. This becomes the "reference" side of the board against which all the other sides will then become either, parallel or at right angles. Next step is to place the reference side against the fence and joint one edge to 90 degrees. We are now thru with the Jointer! We have one face flat and one edge at 90 degrees. I then prefer to go to the Table saw and rip the remaining edge parallel to the "good" edge. Then I can thickness plane the remaining face parallel with the "reference" side or face.
I have watched a friend take a heavy oak 12' x 14" by 3" board and freehand joint in in the manner I described above to flatten one side, by using the tables as levers, he single handedly moves the board across the jointer at only the places that he visually determined needed jointing/planing, until the entire face was flat. Watching this guy you knew that he has done this at least 10 thousand times. All his motions were smooth and fluid, just "git r done".