Flight plans vs ATC

Hi All. Not sure if this is the right forum for this qustion but here goes:

Am learning to proram the PMDG 737 FMC and getting the hang of it, but the problem i have is that the flight plan i am entering is based on real world, rather than the seeded flight planner in FS9.

So, even tho i can load my own Fp into the FMC, ATC (either Radar contact or FS9) are looking at the one i had to create in the FS9 flight planner in order to do an IFR flight instead of a VFR.

Is there any way I can edit the default flight plan provided from the FS9 planner to my own plan without having to edit the text file (.pln file) directly?

Hope someone knows what Im on about

Regards
Grant