There are no sure ways to insure you don't scratch the inside of the tank. I use a Might Magnet scrubber which is similar to the Mag Float. Same concept. I use the MM cleanig pads and their algae sleeves. I also use their Algae Dozer pads which are made for calcareous algae like coraline. The key is being careful if you have a sand bottom and paying close attention to the pad. The sleeves that go over the pads are very helpful in keeping bits of sand away from the acrylic when you get sand caught in the pad.
The good news is that acrylic, unlike glass is very forgiving and you can remove scratches from inside the tank even when the tank is full. It just take the right grades of sand paper and some elbow grease along with a good strong magnet scrubber. My acrylic display is over 20 years old now since I had it made and it still looks damn near perfect after all this time. I've polished it inside and out with a full tank and the scratches are far and few and easily removable. Glass tank owners can rarely say the same.