I am installing 5 1/4 inch baseboards. I have only mitered using boards standing and my saw will not cut this tall. I have access to a 10 inch compound miter saw that says will cut 6 inch baseboards laying flat. Does this work and is it any more difficult? Thanks

Yes it works, and no its not more difficult.

Two things to do first:
1) calibrate the 0 and 45 degree tilt of your saw using a small square or speed square. Your saw's manual should give you directions on how to do this.
2) ensure the trim piece is properly supported along its whole length before you cut it. It will affect the cut angle if it is bent.

Thanks, I'll give it a try today.