He's still trainable. Get him neutered ASAP to help with the marking. Crating is a GOOD thing as long as you give him frequent breaks. Don't worry about being "alpha" just help him to learn the rules, like he sits for his food and attention. Feed them separately or feed him in his crate. Sounds like
this bowl might work well for you if he isn't chewing his food. It slows them down.
When we got Sammy she was almost a year old and peed and pooped wherever she wanted. 6 months later she rarely has an accident. It can be done. We combined crate training with tethering and watching her closely and we still take her out often to avoid the chance of an accident.
You also might need a training class just so you have some help and don't feel so overwhelmed.