APUs are not designed for Crossfire, although it is possible. If I remember correctly, the R7 250 is the most suitable card for that APU because is closely matches the graphical specification. If the dedicated graphics card vastly exceeds the APU, then the card will throttle itself, as dual graphics always use the specification of the lowest performing component.
For the time being, I'd switch the APU graphics off and just use the dedicated graphics card. Switching to an FX-6300 will mean buying a new motherboard, but AMD are releasing new CPUs along with a new socket later this year, so the current AM3+ socket (which the FX-6300 uses) is a dead end. Wait and see what AMD bring to the table before you consider an upgrade. Intel are...