Of the multi output video cards I have had working with CRTEmu, it is always the case that only one of the outputs is Analog and the other outputs are Digital. I am making an assumption here, but I am pretty sure CRTEmu only works on the analog output. So you would either need a video card that has two analog outputs, or run two video cards each with a single analog output.
NOTE: Do not buy anything based on the above info alone...this is all hypothetical. I have not tried to run dual CRTs and wont pretend to know what is going on under the hood of CRTEmu. It could be the case that CRTEmu will only work with a single CRT monitor or with a single Video card. Unless someone with experience attempting this speaks up, you might need to do some testing on your own.
Good luck!