I have done a number of Saturn V builds and have tried a matte finish with poor results due to the decals. Pretty good practice to use gloss on the color coats when waterslide decals are involved and then use a matte clear coat if you wants a matte finish.
There are some decals that go on the black surfaces. Here are a couple pictures of my last #1969 build and you can see the white squares that go in the black portion on the upper transition wrap and the numeral decals that go across the white and black portions on the first stage.
Micro-sol is pretty much mandatory on this build if you want the decals to sit nicely in the little grooves. I used the stick from a q-tip with the cotton removed to set the decals in the grooves then micro-sol to truly blend them in. As others have noted, been using micro-sol for years on almost every build that uses decals. If you need something sharper to push the decals down, I used a rounded toothpick, but you need to be super careful if you do that not to rip the decals. Especially once you have applied micro-sol. Remember that micro-sol is a solvent - it works by breaking down the decal. Once you apply it, the decal is very, very soft and can squish or rip easily. It is awesome stuff, but I highly recommend you practice with some spare decals before you try it on a Saturn V build for the first time. I use paint brushes of various sizes to move, adjust and smooth the decals while manipulating them on the rocket.