Without knowing what machine you are eyeing exactly nobody can advise specifically. Multi-GPU is not bad in general. any issues that may arise come down to specific hardware and driver conflicts and the methods to circumvent or resolve them can vary. Turning off extra GPUs is one way, shuffling around monitor ports in multi-screen environments another and then of course all the "trivial" stuff like changing resolutions. Which of those will apply realyl comes down to all the details - you may need to use all tricks or none at all if your system is already configured perfectly.
Mylenium