I put a new belt on my 94 accord. since then the car runs rough, like it has some faint chatter and acts like 2 lplug wires are crossed. we put the belt on and lined up all the marks. then with the marks on the camshaft (arrow facing up and the two lines on the sides parallel to the head) and the crank pulloey lined up to 0degrees. we set the tension 3 teeth back. A question is, do u set the marks and then tension the belt or do u tension the belt so the marks line up?

 

Sounds like you are out of time, shouldn't be any need to back the belt up that far.
When you install the T-belt, you should have the front side almost as tight as it needs to be, and the slack on the rear side or tensioner side. When you push up the tensioner and tighten it down you can then check the timing marks.