If you don't use the flight planning in MSFS but just start at a gate and program it yourself in de flightcomputer of the Neo. Will ATC use this to guide you?

I want to use the actual (realise) runways and not the (often) wrong RWY MSFS2020 orders you to use. And same with Flightplan. 

Yes, somewhat. If you start at the gate and plan out your flight plan, you can request IFR clearance from ATC and it'll try to work accordingly. The ATC in this sim is very poor overall right now though, so you'll probably have trouble with their altitude assignments and seemingly random approach assignments and vectors that differ from your flight plan. As of right now all we can hope for is an update to make ATC better.