Should I as a GM use ambushes to raise the difficulty of combat as opposed to using higher professional rating NPC's and more enemies to try and test the two?
Be VERY careful whatever you choose.
As a player, I've seen more situations that either should have been a TPK but weren't through shear luck that left us all near dead, or, flat our were TPK, because the GM wanted to make things a little difficult.
It doesn't take much in SR to turn deadly quick.
My take is less is more here.
Don't change any Professional Rating by more than 1.
Don't do it to ALL enemies or the Boss. If its a Boss & 5 Goons, pick 1 goon & make him a Lt./Sidekick at 1 PR higher.
Don't "double or triple" goons. Add 1 extra goon. Start small & increase to 2 after several encounters to see how they do.
Ambushes are just plain mean by removing the dodge roll. I still recall going into a mission where the Enemy sniper dropped me to 1-2 boxes left in a single shot after the GM didn't even give us a surprise roll.
You can always increase in more small amounts as time goes on, but you can't rewind time to resurrect everyone after you wiped the entire group w/o looking bad.