It sounds like you are interested in improving the hull, not just covering it cosmetically. I just did a little bit of reading about the Interlux products. The InterProtect 2000e is a 2-part protection barrier to prevent blistering. If you determine that those dots are actually filled blisters (maybe just surface blisters thru the gelcoat) and assuming that the integrity is sound at all locations, you may be able to simply start with the protection part. Interlux says this product is a good primer for whatever you put over it.
It seems that 3 coats is the usual practice. I would guess that you might do 2 coats of 2000e primer and then finish with 1 coat of vc performance. The characteristics of the vc performance is what you want for a slick bottom, performance bottom that doesn't require anti-fouling. Keep in mind that vc performance is suitable over bare gelcoat or a 2-part primer. But you should not put this over any 1-part paint. So you may just want to put the vc performance over the existing gel coat if you want to economize. I don't know if 1 coat of the vc performance is suitable or if 2 coats is better. I have ablative over barrier. I've been using BottomKote NT, which is described as a "hard" ablative.
The nice part about the vc performance is you can keep a nice clean white bottom if that is what you prefer.
You really should get on the horn with Interlux to get advise how to use these products together. Preparation is always the first, best step! I have had very good luck with every Interlux product that I have used, so I tend to stick with their products for my boat.