You can use a folded towel or a sponge applicator of some kind as long as it will stand up to the work and allow fairly even pressure. You need to use some pressure when doing it (if nothing else than to just keep the applicator from slipping out), but don't overdo it.
Budget lots of time, and have a stronger product like DACP or a Fine Cut product handy. Polishing out swirls by hand is doable, but takes longer, is tough work, and sometimes you have to compensate with a stronger product.
Not sure about having to strip off SG, but you probably don't have to worry about it since any polish is going to remove it.