Thank you, this is what I was looking for. I thought I was just to crate and rotate and continue that forever. I feel that just them being apart might make them forget each other and have more fights when they'd see each other again. I just don't understand marking and treating Nitro for looking at Buddy when he isn't around, how do I go about doing that?
Edit: Also both dogs don't have any spots around the house, the kitchen is just where we're around most.
And another question on crate rotate, what should I do exactly? Separate them by a baby-gate or actually one in the crate, one out?
Absolutely not, necessarily. Crate and rotate is just a term to literally do just that, at least in this moment. It doesn't have to be a forever thing when it is referred to, it will depend on the dogs involved. My Border Collie and GSD pup are being crated and rotated right now, not because of aggression, but because my pup is paying too much attention to my border collie when they are both loose and will not stop pestering him and occasionally blows me off for him. So they don't get to hang out, period, for at least a week. Then after some more training on the pup's behalf, they'll start re-integrating. My border collie shouldn't have to put up with a pesky pup though. He'd RATHER be crated, honestly.
Taking them away from each other is going to be more likely to reset to neutral bounds between the two. Letting them engage in nasty/snarky behavior is going to reinforce it ten-fold. Like with any habit, to have a chance at correcting it permanently, you have to prevent it from happening at all for a lengthy period of time.
The marking and treating, I am referring to when they can see each other, but cannot get near each other, whether that is due to glass doors, leashes, crates, gates, etc. When you know that Buddy will not/can not come near Nitro to instigate a fight (over food) you can mark/treat Nitro for looking at Buddy, thus creating a positive association.
You can use actual crates or gates, whatever you prefer/works easiest, and prevents them from engaging in negative behavior. If they will pick over a gate or stare through/snarl through, I wouldn't use a gate, or double gate an area. Likewise with a crate- if the loose dog can walk up to a crate, I would not use that as a means of confining the cratee. It's going to create a lot of tension and that will not help.
I crated/rotated one dog with a separate group of Three dogs and Three dogs for about 6 months. Roommates three dogs could interact with my safe three, but stayed in a separate spot in the house. Duke could not interact or SEE any of them, period, or he would go batshit crazy. If he ever came into contact with one, he would try to kill it. So we kept two doors between him being crated and any loose dogs at any time. We had him in a spare bedroom, crated, on the far side of the house, with a baby gate in the doorway as well. I would get up in the morning, make sure roommate's dogs had been out already (She got up early/went to bed late) and that her door was closed and their gate was locked (two doors) then I would let my three out, put them in crates in the living room with breakfast, and walk the aggressor on leash outside to the yard to potty and play for about an hour. Then back into his crate with breakfast and my three got to come out for about an hour. Then back into crates and he came out for a few hours, then they did, etc. It is rough for a while, especially if you live with others (I lived with 4 other people) but it does become routine after a while.
So I'll definitely be doing crate/rotate. I'm just worried about a few things, well not worried but questioning.
For C/R, how do I feed them, how do I give them each attention, can they go on walks together, go outside together..?
I would let one out in the morning, bring him back in, feed in his crate. Let the other out, bring him back in, feed in the common area. Give that dog attention for a half hour-hour, and swap.
Personally, with dogs that bicker like this but aren't intent on killing each other all the time, I would do leash walks with them AND ANOTHER PERSON. One handler per dog, always walking parallel, as much as you can. This will be a positive addition to their relationship and neither will be better than the other or have the opportunity to start/end anything.
Good luck.