Most pregnancy and parenting websites recommend a position that is easy on the woman's back that also puts as little pressure as possible on her belly. Girl-on-top would be the most obvious one, but you don't want to let her tire herself out, either.
The most important thing to remember is, if she doesn't feel comfortable while she is doing it, she isn't going to want to do it.
And if she's feeling bad because of hormones, health changes, the fact that she isn't sleeping well, etc, then just leave her well enough alone.
Most women don't lose their sex drive when pregnant, they just don't feel comfortable with their bodies or they feel tired, sick, and stressed.
Only do it if she feels up to it, and try to make her comfortable, and remember that for now, you have to do most of the work. Also remember that everything on her body will feel more sensitive and she will probably feel pain a lot easier, like when she has her period, only worse, so be gentle. And listen to her. If she says "Stop" then stop, because she means it and you don't want to piss off a pregnant lady!