We had three males in the house at one time. Hydrox was our old guy. And then BooBoo and Spike were brothers....they got along well, but they were born together and grew up together. Spike went to the Bridge one week before their first birthday.
Several years ago, we decided to bring in Da-Pumpkin Boy. He was a little stray orange tiger kitten, about four months old, that DH found where he works. So he brought Pumpkin home, took him to the vet for a check-up and to get "de-balled". Pumpkin came home the next day.
We went through hell! (sorry) Pumpkin was a big kitten and, eventually, he would grow into a big cat. And we think BooBoo knew that. Plus BooBoo was domineering. He terrorized that boy and made his life terrible for months and months. It was that bad that the only time Pumpkin could actually play was when we were home to keep an eye on things. When we went to work, we would shut BooBoo, Whisper, and Ms. Pepe in the bedroom, and keep Bootser, Banshee, and Pumpkin in the rest of the house. At least that way, Pumpkin was able to have some peace. I would sit on the couch and cry because I didn't think it was ever going to work out.
And then one morning, I was in the computer room. Pumpkin raced back the hallway with BooBoo hot on his tail. Suddenly Pumpkin stopped dead, took a breath (I could actually hear him), turned around, reared up on his hind legs, and started to box BooBoo's ears! Boo was so surprised, he ran back out of the hallway. Once Pumpkin realized what he did, he went into the bedroom and hid under the bed for about an hour.
But you know what? That was that! From that point on, Boo left Pumpkin alone. We have pictures of them sitting side by side, looking out the glass doors in the kitchen. They were never buddies, but Boo learned to tolerate Pumpkin being around. And Pumpkin really didn't care one way or the other...he just wanted Boo to leave him alone.
Pumpkin developed leukemia when he was about 3 years old. And we lost our boy.
Meanwhile, we've never even tried to bring another male into the house. Always females and always little kittens. Boo is now the only male of our six cats and we think BooBoo enjoys "his" harem.
So I guess what I'm trying to say is that, with a LOT of patience and a LOT of perserverance, maybe your two boys will eventually learn to tolerate each other. They may not ever be best friends, but they'll work it out.