I also have carpet in the trunks of my 5.5 uni.
Be careful when inserting boards in, rear edge can catch on carpet, tearing it out. Key is to make sure top edge of carpet is glued tight, and slide boards down with front (round) edge touching the inside of well, not the back (fine) edge of boards. Once the board sticks out bottom of hull, it's not an issue.
It's easy to glue carpet on front edge, the slot is wider. At the back, it's tricky, since slot is so narrow.