If your defenders are over-commiting, make sure you don't hold L1 when your passing out of defence...it will make them run on ahead of the midfielder that's receiving the pass. If you lose possession in those circumstances the opposition will likely be 1-on-1 against the keeper, with all the space in the world.
You could try Quick Settings to set the Team Strategy to Counter Attack, but it's a bit of a heavy handed way of managing the team. (It seems to set all DF's to High defensive awareness, and Teams Attack/Defence level to auto-defencive.)
Under Formation, look at the List Team Settings option. It'll show you:
the Attack/Defence Level of the side (you want to avoid auto-attack unless your chasing a goal late in a game);
The Defence System, Normal, Line or Sweeper. The Sweeper option should keep one DF covering while the other mark attackers. (I think you can play Sweeper properly without a CBW?);
and the degree of emphasis on certain tactics like the Back Line, pressing the ball, offside and Counter Attacking.
Make sure your not pushing the team's Attack/Defence level too far up (Red) by hitting L2 and R1, keep it around Green to Yellow if your defending a lead late on.
Maybe set your defenders to man-mark the strikers individually?
Or set a DMF's Attack arrows to give cover to the defence by having him cover the width of the pitch in front of them. And put his Mark Settings to CV - covering, so he doesn't wander out position.
It may be worth working on a formation, stocking it, and then fitting other teams into that. Then use Formation -> Automatic Sort -> Change team to suit formation (y/n?) -> Change starting line-up as well (y/n). Double check the selections that the COM makes for players in poor form (blue arrows) who you might want to replace, and scan the subs for anyone who's on top form (red arrows).
At least then you can apply a consitant team shape/strategy to most clubs, and get on with with playing. Better still have a a range that you are comfortable with (a 3-5-2 ,and a 4-4-2 or 4-3-3). Then you can change the shape of a side depending on where the strength's of your squad are, and who's in form. (e.g if yu haven't got 3 decent CBT's playing well, or maybe the SMF players are weak, look to see if you have 2 good SB's)