It is a bit complicated to understand the allign planes MFD, i which direction should i engage thrust. I am not understanding the allign planes mfd.
To align your planes with a target (you've set one, right?) you need to burn normal (ie, at right angles) to your orbital plane at either the ascending node (marked by AN) or at the descending node (marked by DN). Your can do either one since for a roughly circular orbit, the delta-v required at each node will be roughly the same.
If you are burning at the ascending node, you need to burn anti-normal, ie, use the "Normal -" autopilot to point in the right direction before burning. Just remember
Anti-
Normal at the
Ascending
Node (AN-AN).
If your are burning at the descending node, you need to burn normal, ie use the "Normal +" autopilot to point in the right direction before burning.
The flashing "Engage Thrust" light will come on when "Tn" (time to node) is approximately half "Est Thrust T" (estimated required thrusting time).
Burn until the "Kill Thrust" light comes on. It may take more than one attempt to get "RInc" down to zero, ie, more than one node, especially if you have a large relative inclination. If it is not zero after the first attempt, fly around to the next node and try again.
Have you done this tutorial?
[ame="http://www.orbithangar.com/searchid.php?ID=3074"]Tutorial: DG to ISS[/ame]
Have you read Go Play In Space?
Do you know why you are aligning planes?