You are way over-thinking this. It seems complicated because you haven't done this before. With practice and experience, it will become 2nd nature to you.
Of course, you should not use your good balls to start learning surface changes. Use and older ball and test it by throwing it after you make changes.
Most surface techniques published by manufacturers are NOT the way they do it in the factory. They are ways they suggest that you can use to closely emulate the factory process. This is also why many people with spinners put their own surface on every new ball; this allows them to replicate their starting process when it becomes necessary to maintain the surface. Some factory finishes are or can be extremely hard to replicate.
Always have a spray bottle of water on hand. Spray the pad and spray the ball while spinning it. You DO NOT want to breathe in resin dust! Plus the water acts as a lubricant and way to stablize the process. You need the have 3 sides of something around the spinner to prevent splashing of water and slurry and polish.
1 Surface:
If you're making a change, you should have some concept of what your starting point is.
So, if the ball is at 3000 grit, is it at 500/3000 or is it at 500/1000/2000/3000 grit. The idea is if you know where you're starting, then you know how to get to where you want to be.
If it's 500/3000 and you want to go to 500/4000, then redo the 500 grit base and then applying the 4000 grit pad.
If it's 500/3000 and you want to go to 500/3000/4000, just apply the 4000 grit pad.
If it's 500/3000 and you want to go to 500/1000/2000/4000, then do that whole sequence.
Those are not all possibilities. You should be able to extrapolate for any other surface you want for those examples.
As for 6 sides, that may be excessive for every surface change. You may want to do that for a total reset of the surface, especially with lower grits. Otherwise, with growing experience, 2 or 4 sides will be perfectly sufficient in most cases.
2. Polish:
This can be tricky. All polishes use micro-abrasives to achieve the shine or gloss you see. Polish is NOT a coating like paint or varnish. It is a modification of the surface.
All polishes have varying degrees of micro-abrasives in them, in different sizes and different quantities. You should, again, know where your starting point is. In the extreme, polish over 500 grit is vastly different from polish over 4000 grit. Different polishes will change the underlying base grit on which you are applying the polish to different results. Usually the glossier or more polished the appearance, the finer the grit level of the resulting surface will be. Most balls, that appear polished, have grit levels of around 5000 or more. 99% will be from 4500 - 6000 grit.
(An over used 4000 grit pad will make a ball, starting around 2000 grit base level, appear polished BECAUSE the used 4000 pad has become 5000 - 6000 grit through wear. This is also how you know a used 4000 grit pad is used up.)
The more polish you apply, the higher the gloss & the higher the final grit.
The more time you spin it, the higher the gloss & the higher the final grit.
The more pressure you apply, the higher the gloss & the higher the final grit.
There are a lot of human factor variables here. Add in the different types of polishes, add in the potentially different base grit and you can see you need to practice and understand through experience, what you're doing. Once you do this, you'll hardly give it a 2nd thought and just proceed because you know where you are and where you want to be.
