I recently did this.
If you don't cut them, then when you fold down the top the seals will pull out of their channels around the hinges. And you have to cut them all the way through, not just the lips of the seals.
The right spot to cut the elbow is straight forward. However, depending upon how many shims there are under the soft top mounting, you may find that the bottom of the vertical seal appears too long and catches the door seal. I would not cut it there right away. Instead, I put a little silicone grease along the channel for the vertical seal to allow the seal to adapt, move, compress, etc.
In my experience the right spot to cut it for the top hinge is a little trickier to get just right. I noticed that the cuts in the horizontal arm of my old seals were not directly in line with the top hinge and had probably moved over time.
I put a little silicone grease in the top channels so that the seal could move a little. I cut the elbow first. Then with the entire seal in place but the top segment still uncut, I partially opened and closed the top. Each time that I flexed the top hinge, I would have to put the seal back into its channel around the hinge. After a few times I was satisfied that the seal had found its happy resting place, and I cut it in line with the hinge.
Maybe overkill?