Step 1:
Wipe down all surfaces that you will be doing repairs to with either warm water or a specialized acrylic cleaner.
Step 2:
Mist a workable area of scratches (maybe a maximum of 6in diameter at a time) begin sanding down the scratches (in a circular motion and with little force) with the 1000 grit wet sandpaper. You can wet the sandpaper a little as well, it won't hurt to do so. Also, you will know if the acrylic is too wet because there should be (even though it is 1600 grit sandpaper) a sense of abrasion.
3. Continually sand the area until the scratches have disappeared or are just BARELY visible and make sure that while sanding you are constantly wiping down the working area to remove the acrylic particle build up and spray the sandpaper as well to remove the acrylic from the sandpaper.
4. Once the scratches are gone or just BARELY visible, switch to the 1600 grit sandpaper.
5. Use the same methods with the 1600 grit as you were with the 1000 grit sandpaper (i.e continual misting, spraying the sandpaper clean and the acrylic as well) until the area is smooth. You WILL still see scratches swirl marks from the sandpaper even with 1600 grit sandpaper. What you are doing here is trying to make the acrylic as smooth as possible in preparation of using the Novus compounds.
6. Once you are done sanding, wipe the area THOROUGHLY to remove any remaining acrylic build up or anything else that is within the working area.
7. Get your drill with the buffing wheel attached to it and apply Novus 3 compound, liberally, to the outer edges of the wheel.
8. On a fairly slow speed, start working the Novus 3 compound around the sanded areas. Use the outer edges of the foam buffing wheel, do not lay it flat on the acrylic and do not press the drill hard against the acrylic because this causes excess friction (which produces heat) and could cloud the acrylic.
9. If you sanded the areas correctly, you shouldn't have to use the Novus 3 compound long. You will be able to tell that you can move on to the Novus 2 compound when the acrylic is cloudy, but reasonably see through and there are only the tiniest of scratches. I mean no scratches thicker than a hair on your head.
10. Finally, attach the other foam buffing wheel to the drill, apply Novus 2 to the edge of the buffing wheel and repeat step 8. Remember, the less foam buffing wheel on the surface of the acrylic, the less friction and heat generated. That is why you should use the edge of the wheel only.
11. At this point, if all is done correctly, the Novus 2 removes the tiniest scratches left behind by the Novus 3 compound and brings your acrylic back to its original beautiful smoothness. Less the scratches.
Notes:
1. It is important to keep in mind that at no time (maybe expect using the 1000 grit ONLY) should you be applying force to the drill or sandpaper. At any time you could cause too much heat and the will cloud the acryic.
2. Continually wet the acrylic in which you are sanding. You are using wet sandpaper and therefore need to keep it wet for it to not excessively damage the acrylic AND to work properly.
3. Remember to use clean rags (cotton most preferred) when wiping down the acrylic. You don't want to contaminate when you think you are wiping the area clean.
4. Most importantly, don't freak out if you still see scratches when you are done. You can go back to the Novus 3 or even the 1600 grit and work the scratches you still saw when you were done. As long as you don't jackhammer into the acrylic, most scratches you caused with the sandpaper are repairable by repeating the steps.