The management fee will go toward the safety net so if your level is $1000 and you've already up to $500 of it then you won't get anything back for the first $500.
What's left would be approx $1300 of which I'm not totally sure of the amount but I'd assume you would get most of that back as you would be over the safety net.
Good news is that for the rest of the year you will get almost all of your medical expenses back for anything. Once we hit the safety net during my PG with Caleb I only had to pay about $5 for my OB checkups and for any other Drs appt for the rest of the year.