Hi GP,
If I understand your request correctly, you have calculated your correction angles, but as to the best of my knowledge FSX does not provide the opportunity to insert these into its flight planner, then it will only give you the actual 'track' to fly, not the heading you must adopt to achieve this track, so you will have to adjust the track with your correction angle(make sure you apply it in the correct direction)and fly this corrected heading.
By all means use auto pilot for your corrected heading(not track).
As you are using real weather update, wind correction angles will vary with altitude, so you will have to calculate new correction angles for your selected altitude ranges. If you are prepared to do this and reset the A/P as your A/C climbs and descends into each range, then all should go well.
Altitude hold will of course only be useful at cruise levels and will have no effect on heading, so by all means use it in cruise.
Bill