If you are booked under one reservation (even if they said party of 6, 2 tables of 3.) then you will get the auto tip.
If you had 2 ressies but the restaurant is willing to seat you together, you will get the auto tip.
You can still leave cash, but it has to be the amount (or more than) that is listed as your required tip.
If you have 2 checks then each check will still inclued it's portion of the tip. ie: your parents will get a tip bill for their 2 meals, and you will get a tip bill for your 4 meals.
Hope that helps a little