We always get gift cards for places like Applebees, Chilis and Olive Garden from our rewards credit card and as gifts from some family members. We always use part of the gift card value as the tip.
Yesterday when DD and I went to Olive Garden, I had a $40 gift card and I bill was about $20. I paid with the gift card, and the server brought back a receipt for me to sign, and it said "Gift card balance before tip $19.63" or whatever the amount was. Then on the receipt there was a place to add the tip and total it, just like when you pay with a credit card. I added the tip amount ($4.00 if it matters) and wrote the total on the slip.
When we go back, the balance on the card will be $15.63 and we will apply that amount to the bill for that trip.
A gift certificate should work just like cash. Some restaurants may deal with thsi differntly, so ask the server if you aren't sure.