I was thinking about using both, but I was wondering if there were any conflicts between say what the ATC tells you and what FSCaptain tells you,does FSCaptain do things like tell you which runways to use etc?

There should be no conflict between the two, FSCaptain doesn't really concern itself with SIDs or STARs, i haven't used RC in sometime but the only possible conflict i can think of would be on Parking gate, FSCaptain can assign a parking gate, not sure if RC4 does or doesn't.  In any case you can disable FSC parking gate ability.  

 

It doesn't tell you what runway to use, it does provide runway information based on weather.

 

I can strongly recommend FSCaptain it's a very good add on and very well supported.  There is a free demo available.

RC is an absolute must if you fly IFR in the heavies...it's a fantastic program.  FSCaptain adds a new level of realism and adds purpose to some flights that otherwise I might not finish.  They are both wonderful programs.   FSCaptain does not tell you which runways to use....for that I would recommend one of the absolute best free gifts to FSX.........www.simbrief.com.  Almost as good as PFPX and will tell you which runways to takeoff and land on.