For the past few years we've eaten many times with a party of 11. The waitstaff has never been anything but accomodating upon our requests for separate checks. We usually inform them before ordering that we would like separate checks, then again before the check is prepared. This request is sometimes met with the "eye-roll", at non-Disney restaurants, but we've NEVER received one at a Disney restaurant.
Just be aware that they will sometimes include the gratuity on large parties, even if separate checks are prepared. I just hate it when I look over my bill later and discover I've tipped them TWICE, to the tune of about 48%....LOL