With the FBQ connected to your mixer’s sub out, you won’t be able to do both sub EQ and feedback eliminating (at least, none above the crossover frequency). To do both, you would have to connect the EQ in front of your crossover. Naturally, any 30-90 Hz boost you do with it connected like that will affect the main speakers as well as the subs.
Another option, if your mixer has an insert for the mic channel, you could patch one channel of the FBQ there, and use the other channel for the sub out, as you have done now.
Also, when you say you want to boost between 30-90 Hz, that’s pretty much the full range of the sub, isn’t it? Why not just turn the sub up?