First a comment; jointing an edge first gains you nothing in my opinion. The edge is not adequate to work as a reference surface for the ensuing operation. That being said, jointing removes irregularities by the nature of the operation. The difference between the highest and lowest spot on the surface will be the amount removed. There are a number of ways to minimize the amount removed or the time to do so. If the material is close to the finished size required, all irregular material will need to be removed. This can be quite wasteful and so I select the least irregular piece that will meet my needs for size and appearance.
If the piece is too irregular to handle effectively I will mount "runners" to the sides to allow me to better control the material.
These runners being nearly true can be quickly milled on the jointer. I will sometimes use these runners to rest against the bandsaw fence to resaw off the lion's share of the waste before tasking my jointer with the balance of the work. If the piece is not too bad I will simply resaw by eye if I can end up with a flatter surface than I am starting with. Once the bulk of the waste is removed, I take the work to the jointer and proceed as normal.
If the blank will be made into smaller parts, I would break it down into oversized pieces first. This lessens the length and width of the parts and therefor minimizes the irregularities per specific piece. The smaller (or the already prepared larger piece can then follow these steps (some variations in order exist per the individual):
1. joint one face.
2. joint one edge perpendicular to that face.
3. plane to thickness.
4. rip to width.
5. crosscut to length.
For a piece longer than your infeed table it is critical that the material be supported as if the table were long enough to support it (roller stands, whatever). If you try to joint material that hangs below the plane of the infeed table, therefor climbs up the infeed table edge as it travels through the feed path and then drops lower than the outfeed table once it has passed that point of support, you'll never get a flat board. The jointer tries to make irregularities match a constant reference surface in the feed path. If that reference surface is not constant, the machine is incapable of reacting to that or correcting for it.
All in all a simple machine but, because of this simplicity, it expects certain things to be a forgone conclusion. Assuming a properly aligned machine, proper feed path is probably priority 1 with feed technique a close 2nd ;-)