You may be better serve by using protein specific tools like Rosetta, or Glide's (Schrodinger) Peptide mode.

[Note: I haven't actually tried this]

I Don't think there are any programs that will simultaneously dock multiple ligands. If you think about it from the prospective of a rate reaction you can see why and your way around it.

3rd order rate are practically non-existent but we see all the time sequential 1st and/or 2nd order reactions.

The the same is true for proteins with that require more than one ligand for actively - one interaction happens first, then the other. In some cases the order matters, in others it does not.

If you have a (final) Holo form of the receptor structure you can probably get away with Docking one peptide incorporating the results into a new set of structures then docking the other peptide against the new set. If you don't know the binding order be sure to check both directions.  -------- Be aware that your Error will be much larger (~nx2) than a single docking. EX:

run1, RECEPTOR= receptor1, LIGAND=ligand1.

open run1 receptor and outputs as individual structures, save as single pdbqt with both receptor and ligand (you can do this in ADT, but if you have trouble you can also use pymol.

run2 RECEPTOR= receptor1+ligand1 positionA, Ligand=ligand2.

IF you do not have a Holo form you will probably need to include some backbone adjustments in between steps (consider some kind of solvated energy minimization) --though some other programs offer an "induce fit" docking that may (or may not) take care of this.

Please go through the following link

Article Multiple Ligand Simultaneous Docking: Orchestrated Dancing o...

It's better to use flexpepdock (highly recommended ) or haddock for peptide and protein docking! !