I find with severe crowding cases, I have to gradually complete IPR (instead of completing it all at once) due to limited access to the true mesial and distal surfaces of the the teeth. This is also much nicer on the patient, both comfort wise and aesthetically as you are able to achieve best tooth contour. This is particularly relevant when larger amounts of IPR is required (>0.4mm-0.5mm).
I tend to start the IPR process from aligner #1 by checking to ensure there is adequate spacing with a yellow (thinnest) IPR strip. Once access to the mesial/distal of the tooth is achieved, I start completed about 01mm-0.2mm of IPR at each visit until the total required is achieved.
Of course, recording what has been completed at each visit is quite important to track quantity of IPR. I generally do this both on the physical treatment overview sheet and in the patients notes.