You're doing a drift shuffle.
If you look at the tope of your CRP-5 you'll notice that it says 'true heading' not 'true track.' When you first put the 90 under the true heading that's wrong, you've lined up the track with the heading marker. This doesn't take into account any drift.
To resolve this you have to do a drift shuffle, which is the process described in your explanation. Check the drift on the centre bit and then rotate the wheel in the same direction until the true track is on the relevant number. In your example you had 12 starboard drift, so you have to put 90 under 12. Then you have to check the drift again. Has it changed? In your case it had - it had changed to 13. Do the same process, move the 90 under 13. You keep 'shuffling' like this until it all lines up (i.e. the 90 is under the 13, and the drift shows as 13), then the value under the 'true heading' is the heading you have to fly to make good that track.
Remarkably difficult to explain via text, but if you google the CRP-5 drift shuffle you'll get better explanations.