yes, if you are using a dedicated video card, the onboard goes unused.
you don;t need to disable it in the BIOS though. the PC will see there is a PCI card connected and automatically take care of that.
integrated GPUs arent expensive though. so you are unlikely to save much by getting a board without one.
In fact, IGP boards tend to be less expensive because they are intended for budget builds.
Compare these two motherboards:
AMD models are pretty much the same.