Do a test seeing you have the choice.
My opinion is that MPE does more and has different functionality and purpose.
I've been using the demo for a few weeks and that would be my advice also. However, here's a quote from the manual:
"It is recommended that you use Codec Suite Sequence presets on CS5. Only then you will
get the benefits of smart rendering for MPEG-1/2, DVCPRO and AVC-Intra. Furthermore,
using presets that are based on Codec Suite editing modes will ensure best performance
since Codec Suite's player and its importers are designed for optimum cooperation."
That seems to imply that you use MC options from "cradle to grave": sequence settings and the MC player explicitly and possibly the MC renderer also.
What I use is the "MC (CUDA)" renderer instead of MPE. I assume that it works with all the CUDA-enabled FX and transitions, since I haven't seen any performance loss, when compared to using the MPE. Maybe someone from Adobe could chime in here, because I'm guessing that the MC CUDA renderer is possibly just an officially tweaked version of the MPE renderer.
Your best bet to find out the answer for sure is to contact MC support.