The R7 240 is an extremely weak graphics card as is the integrated card on your APU. The BEST option would be to sell the 240s and but an RX 460 for $100, as you would have over twice the performance you have now without any drawbacks of multiple GPUs. But if you don't want to do that, then disable the GPU on your APU in BIOS and run with the 2 240s in Crossfire.
I suggest you to use both r7 240 for crossfire and disable APU graphics in BIOS, if it possible.
But some games have graphical anomalies on multi gpu systems.