When I adjust an indexed rear derailleur, I start with it in the smallest cog. I'll adjust the index screw for that gear (it may be marked H for high gear) so that the derailleur pulleys are directly in line with the small cog, looking at it from the back. (Also, when looking from the back, if the derailleur pulleys are not straight up and down, something is bent and will screw up your shifting.) After setting the limit screw, I then make sure all the slack is taken out of the derailleur cable. Usually, that is all I need to do to get the indexing to work properly.

If something is off after all that, I would check to see whether the cable is clamped properly to the derailleur. If the route the cable takes to the clamp is wrong, the cable pull will be off just enough for the indexing to fail.