Marinara sauce isn't ideal for pizza for the very reason you describe - it's too watery. Pasta sauces need to be runny enough to coat a great deal of surface area, also pasta will absorb a bit of water from the sauce even when fully cooked. A pizza has very little surface area compared to pasta, and the base isn't going to absorb much liquid so a thicker sauce is better.
Canned tomatoes vary in the amount of water in them, good quality tomatoes won't have added water, but the tomatoes may have a higher water content depending on a number of factors. Some tomatoes are thick enough to use for pizza straight out of the can, others need a bit of help. If it's not thick enough you can:
- Cook the sauce down, uncovered to boil off the water. This is effective but takes time, how long depends on how much water needs to evaporate
- Add tomato paste. A dab of good quality tomato paste will add some zesty flavor, and it's very quick. Just remember to add it at the beginning to some oil and fry it off to get rid of any bitter flavors
I personally use the second method and my pizza sauce takes all of 10 minutes to make. It's a squirt of tomato paste (it comes in tubes in the UK), a clove of garlic, a can of plain italian chopped tomatoes, a pinch of herbs, a small dab of honey, and a twist of fresh pepper. I fry off the paste in some olive oil along with the garlic, then add everything else and simmer for 5 minutes and comes out great every single time. I know of people who crush whole tomatoes and cook them for a couple of hours and they don't get a better result - it's the quality of the tomatoes that makes the difference.