Welcome to the world of milling, and now working from your "other" wood pile.
I do not have a join(t)er, but I still make flat boards, albiet shorter ones. One option is to find a 2x10 that is really flat, then attach your rough lumber to it... I've used hot glue, and screws. I then run the flat 2x10 against the fence of my band saw (12" depth of cut) to make one flat face. The planer can make your second face. Likewise, attach a long straight edge to the now flat board, and make a straight edge on your board with your table saw using the attached straight edge against the fence.
I've found that hot glue is actually pretty good at holding wood in place. Put it in the areas where it stays thicker (not right where the rough cut wood meets the 2x10) and it will be easier to cut off. I'd be willing to try running it through the planer this way too. If you use screws, just countersink them below what ever blade they will be passing by, but don't over tighten them, or you will warp the board, and it will re-warp when you detach it from the straight edge (if it remained straight). I usually screw my flatened board to the straight edge as I mentioned above for the table saw step.
Depending on the size of the boards, if you have bigger board than planer, you might consider a hand held power planer (Makita N1900b is one option). I find these to be really handy to work on large boards, and to take off the outer layer of wood that usually contains dirt and stuff that has been blown onto them while drying. This dirt is so hard on blades and stuff that I take it off with the planer before anything. The planer has carbide blades that are easily replaceable (or sharpenable if you have diamond stones).
If you need shorter pieces of wood, rough cut them out first, and use your most warped pieces if the grain works for your project... short boards take less work to true up.
Hope that helps.
P.S. The Makita is good for rough planing, you will have to use a hand planer or belt sander to make the board really smooth.