Yes, they will. All the 3rd placed teams from the EL group stages.
I know why they do it that way (keeps virtually all the games meaningful for both teams), but the criss-crossing between the competitions really sucks.
Given that lack of quality competition European games is a problem for the minnow sides and fixture pileup is a problem for the bigger sides, they should really do the group stage at an earlier point in the competition.
Do a brief qualifying stage to fish out the Andorran sides, and then let everybody below those top 5 leagues do a full group stage with the top 2 qualifying for a Round of 64 playing two-legged ties to the finish.