Well,
explain a little more could be pages.
In short. I always use the generic/standard rules, whatever it is called. The meaning behind that is.
You have the "Tax & Calculation Rules", everything in there is controlled by categories, shopper groups, whatever.
So if your calculation is not right, you have to check your rules. If you have 35% instead of 21%, maybe your 12% have been added for some reason to your 21% rules, because of some rule, that might be applied to "ALL" categories/groups or so.
If you have applied 12% for a category "food" and to the category "tax 12" and your product has both groups, it will be applied two times. So to use the generic rules, it is best to disable all rules first and slowly extend it one by one. It is a whole new thinking process if you are used to the old VM2 rules. Bammm, fixed 21% VAT, bammm, my discount below, finished. You can still do that, but if you want to have a complicated system like yours, you have to make a nice drawing on a white piece of paper first and get the picture of the whole system.
Every system is different, so this is not explained easily in a "general" way.
Hope, this was not too confusing
Stefan