I am currently using FSCommander, and it allows me to save my flight plan to PMDG's native .RTE format. Is there a better one that will allow me to do the same thing?

I use Aivlasoft EFB for all my flights, including PMDG birds.  Although I've never used FSC, I've seen videos of it and prefer the much cleaner and neater look of Aivlasofts.  You can run it windowed (I didn't much care for that) or you can network another machine (like I do) to the FSX machine for a multi-monitor setup.  I'm not sure if FSC works the same way, but Aivlasoft's EFB does everything I need it to with a more modern feel.  There's a 30 day free trial if you're interested.

I didn't know you can use Aviasoft EFB for flight planning.

I dont really think that Aivlasofts EFB is that much better than FSC, they both do the same thing really.

Aivlasoft EFB has a much cleaner interface