I don't know much about how Madden 07 has rated the Cowboys defensive players, but if they run a 3-4, you may want to check and see if a 3-4 would get better players on the field more often. (That is, do they have 4 good LBs and one good DT? Probably, and you'll want to run a 3-4. If they have a good second DT a 4-3 won't hurt, but that may not be the case.)
With a 3-4, you should expect to blitz at least one LB every play that you want to get any pressure on the QB. A three man rush will rarely get any pressure, as I'm sure you've seen. Real NFL defenses do this as well. The benefit of the 3-4 is that if you have 4 good LBs, you can blitz one or two of them each down and the offensive line will have to read who the extra rushers are. The LB defensive audibles will let you pick this from the line of scrimmage as well.
While you'll want to stick to your core defensive set most of the time, if they're bringing out a lot of WRs you'll want to learn some good defenses out of the Nickel and Dime sets. As good as your 3-4 playcall may be, his WRs will probably still burn your LBs more often than not. Again, if you wait to see his set every time before you pick a play, you'll have the info you need.
For example, I play as the Seahawks most of the time, and run a 4-3 as my default set. If I play someone who is killing me with the run, I'll run some safety blitzes in the 4-3 to get more men in the box or I'll go with a 46 defense. If I see him coming out with 3WR, I'll sometimes switch to a Nickel, sometimes keep it 4-3, that's a grey area and it's all about the situation. If I see 4 or 5 WR, I bring in an extra DB or two. I may blitz one or two of those DBs, maybe not, but the fact that they're out there in coverage pre-snap doesn't give the opponent the idea that they can burn me as they would if they see my LBs drift out. This way, they have to take a little extra time to read the blitz before knowing the right way to go.
So yeah, take a look at your personnel and learn some "bread and butter" plays in that set, but then learn some Nickel and Dime coverages (at least one or two each of man and zone, and a few blitzes) and use those when those extra WRs come out and you think he's actually passing. Hope this helps!