Hello and welcome to Binky Bunny. Click on the BUNNY INFO link at the top of the page for some great information on the basics of bunny care – feeding, housing, litter training, etc.
As far as I know, a male rabbit is no more territorial than a female rabbit. To control certain behaviors, as well as for health reasons, it is recommended that you spay or neuter a rabbit. You will need to find a rabbit savvy vet in your area to do that, as well as to have for any medical problems that arise. If you are trying to litter box train your rabbit (which may not be completely successful until it has been spayed or neutered) you should not have any bedding in the rest of the cage. That confuses them. You should only have rabbit appropriate litter in the litter box. For bedding, you can use fleece blankets. Just watch for chewing. It is okay for rabbits to eat some cardboard, but you don’t want them to consume a lot of it.
Most rabbits prefer a water bowl to a water bottle. They can access the water better with a bowl. A heavy crockery bowl is best.
Since the rabbit is 12 weeks old, you could still give it alfalfa hay, along with alfalfa based pellets, but it is a good idea to go ahead and introduce grass hays, such as timothy or orchard grass. There are lists of good veggies and how often to give them in the BUNNY INFO link. You really need to start slowly with any veggies, and not give too much fruit as it can cause gas and GI upset.
A Californian is a large breed of rabbit, so be sure that the crate is large enough. Your rabbit will still need some hours of out of cage time every day for exercise, in a bunny proofed room.