you should submit your application according to the deadlines of whatever round you're applying in. if you're applying in a round whose deadline isn't until after you re-take the exam, then you may want to wait until you re-take the exam to submit your application materials.

still, it shouldn't matter too much. when you apply, you'll have space on the application in which to indicate pending GMAT administrations. in other words, if your application materials are received before your next gmat administration, the school will know that you're going to re-take the test, because you'll write as much on the application.

just to make sure, though, i would wait until after the re-take, if the round deadline will allow you to do so.