Same as with anyone else I ride with. Pull up to the stop sign. Stop. They should be right next to you. Both of you go through at the same time with her about a half a bike length behind and to the right. That's just the way I roll. Same thing if it was a guy.
Being a gentleman, I wait for my GF to pull out beside me, unless she is leading and then we take off from the stop sign together. She is an excellent rider, so I never have to wait for her or vice-versa.
O.L is not 100% comfortable riding side by side yet, especially in a lot of traffic. So she is usually 3/4 bike length back. SO i come to a stop and if its clear i go ahead, usually that will just leave her doing a slow and go. If she is to far back, i will wait for her. But as her confidence grows, the less i even have to think about that.