You have to back down the weight if you're doing paused squats, especially with longer (5-7 seconds) pauses. Paused squats are great for learning how to keep proper tightness, and how to position yourself in the hole to be as strong as possible.
However, you're doing starting strenght and squatting 3 times a week. I would be careful with adding more volume than the original program. You will certainly get stronger without doing any paused squats, but if you have to do it, keep it to a minimum so it doesn't mess with your recovery.