Applying for montgomery gi bill while waiting for buy up

I am separating from the military in a few months. In my particular situation, I will be financially better off using the Montgomery GI bill over the post 9/11. I submitted the buy up paperwork to finance who said they'll take the $600 out of my next LES. Can I submit the GI bill application on VA.gov now to get the ball rolling, is there a way to update when my buy up is deducted, or should I wait till I have my next LES?