I had this recently in a not so well structured event (not my structure I hasten to add!) The way we did it was to include the 500's as part of the 100 race, buying as much as possible into one stack so that each player did not have much left to race off, but there would be circumstance where it would be necessary to issue 9 cards to one player, albeit rare.
We didn't have any issues doing it that way and we did not run out of cards during any of the races, either, so all in all, a decent way of getting both chips off.
There would be nothing wrong I suppose in carrying out two races at each table, 100's then 500's either though.
Regards
Stu