I have recently found that my opening strategy has been improving as I study openings, and I'm sure that it will still get better.  What I find now is that I get through the openings and I do not know what to do next to use my peices effectively.  Sometimes due to the opening I use, I am unable to use peices to the best of their potential, and even when I can, I don't see moves that I should. 

How can I get better at seeing moves that could increase my winning chances, in addition to the tactics trainer?

Zredfire, one thing I hear a lot because im in same problem your in is to just play as many games as you can. Look at weaknesses in his pawn structure and find good outposts for your knights.

Heres a good article to read.

http://www.chesscafe.com/text/heisman04.pdf

Id advise studying tactics if you know the opening principles well.

Which opening theory books have you read?

Zredfire

I think you just answered your own question. The way to get better at the middle game and improve your entire chess game is to plow through hundreds of chess puzzles.

The puzzles giving you dozens and dozens of situations where you have to recognize there is an advantage for one side or the other, but it's not obvious because the board is cluttered with pieces (middle game) and/or material is equal. You practice the situations over and over, and after like doing a thousand of them, you commit them to your internal memory. 

Now all of a sudden, you play a game, and boom! positions arise that are nearly identical to the ones you studied, and now automatically and instinctively know what to do.

Other than chess puzzles, another thing you can do is have your games analyzed by the computer or a better chess player so you can figure out the exact point in the game where things went wrong so that you can fix it, and not make the same mistake next game. I hope this helps :)

I'm totally in the same boat.  Going through the tactics trainer has been very helpful for me -- I found that I was terrible at the problems, but am slowly improving.  Seemed like at first it was hard to keep it over the 700 range puzzles, then it was the 800 range, now I'm finally pushing over the 1000 range...  It's funny, if I do problems in the morning I find I can react much quicker, towards the end of the day and I get frustrated with simpler problems.

Not to sound too much like a sales-pitch for the site, but Chess Mentor has been extremely helpful for me.  It's scary how many situations I'm starting to see in games that I'm playing that are similar to what's in the Mentor lessons.  Of course, pulling them off in a game is another matter...

Zredfire, I greatly enjoyed our game together. I also recommend reviewing the PGN files of your games, both won and lost, post the games in the forums, make use of the free computer analysis this site provides, review other players games, and try chess mentor.  Look at some of the higher rated players games, or some of the articles showing games between GM's. Look at each move and try to understand why the move was made, what was the threat or tactic that was to be used. Last of all, if you have any questions, ask in the forums.

Some VERY general advice to give you is

1.  If you are winning on one side of the board and the other side of the board is unclear play to prevent any counterplay or create another weakness on the other side and or in the center.  If you are  

2.  Figure out if you are actually recognizing where your advantages and weaknesses lies

3.  Closely related to 2.  Is the opening you are playing suited to your style of play.  Maybe the reason you don't know where to go is because you are playing the kings gambit when you are a positional player(most obvious example I could think of).   

4.  limit weaknesses in your own position(duh).  But, if you can exchange a weakness for an advantage elsewhere sometimes it is beneficial(especially if your weakness is in a position where the opposition can not exploit it