1. You can set one of your defenders to spy the QB to help with them always scrambling. On PS3 you select the defender you want to use as your spy (usually a corner with high tackle rating or a fast LB) then press X for "hot route" and then I believe its left on the left stick. Also you can set your D-line to contain by pressing L1 and then up on your left stick (again thats on PS3)
2. If the guy is running right up the middle on you over and over you need to stack the box to stop the run. You can do this in any formation. If you stay in the base 4-3 you already have 7 defenders in down in the box to stop the run and you can manually bring down a safety or pick a play where a safety or corner blitzes. I'm sure you watched the Super Bowl? Think of how Cam Chancellor for the Seahawks plays, he usually comes down to 1-3 yards behind the linebackers to help stop the run.
Offense is a lot easier because you have the element of surprise on your side. If they're guessing your plays my bet is you call the same 5-6 plays over and over. You need to sprinkle in both the run and the pass. If you prefer to run the ball more thats fine, but you need to mix in play action passes and some short slant routes just to loosen up the defense and make them back off the run. If you prefer to throw the ball more often then mix in some draw plays and dives/sweeps out of whatever shotgun formation you use the most.