Yes, neutering is okay, and yes it may (no guarantees) prevent marking, but it usually takes a few weeks for the male hormones to disappear. If you're not having problems now though, you probably won't. Marking may occur if you bring in another dog, especially a male - even if they're neutered. Being vigilant and cleaning up any incidents immediately with something designed to eliminate odor, will help to stop that kind of thing.
Neutering as a preventative to health problems is always a good idea, at any age.
For your question about housebreaking when he's used to papertraining - how about putting the paper outside and encouraging him to go in that one spot. Once he identifies with the spot, remove or decrease the newspaper. But do be sure to keep the newspaper you're reading off the floor.
