Do you have a guinea pig savvy vet? If not, you need to find one. There are vet recommendations for various areas on this site. If your area is not listed, then what I did was call quite a few vets that I knew were reputable and asked them, "Who would you recommend as having the most experience with guinea pigs?" Note that I did NOT ask, "Do you see guinea pigs?" or "Do you have experience with guinea pigs?" since "experience" could be defined as "I saw one once 12 years ago" in some vets' minds if they really want your business.
But, asking who they know has the MOST experience is an objective question and does not cast any aspersions on their own ability. When I kept hearing the same vet being recommended over and over again, that's who I went with and it was a good choice.
When we had our babies, we guessed the sex wrongly on two or three of them. I am so glad we took all our babies to the savvy vet to get double-checked! I recommend you do the same.
Also, for future reference, please break up your paragraphs into easier to read shorter spurts like I've done here. Makes it so much easier to read, and it will increase the likelihood of other people taking the time to respond.
That said, we put our male babies in with their dad at three weeks. He himself was about 6 months old at the time. They did very well together. The babies were comforted at losing their mommas, and dad did a good job teaching them how to be a guinea pig. When they were first put together, he stuck his nose under each of their rumps (probably determining sex) and lifted their rumps off the ground even. A bit later they tried to nurse from him, but he put a stop to that with some nips, and that was that.
We re-homed our male babies at two months old. We neutered our male and he lives in the herd of the rest of our females now.
Whether you put the male babies in with the skinny (be CERTAIN he is male first!) or their dad, that is up to you and your observations of them. I doubt that dad will be outright mean to the babies at 3 weeks. Even a teenaged guinea pig does not see 3 week old babies as threats.
Do you think there could be a chance in the future we could put the male and the skinny together? Maybe after they have both gone through the teenage time? or shold we plan for them to always be separate? I just don't want one or the other to have to be by themself forever.
Also another route if we decided to get the male or the skinny (if he is truly a male) neutered, what is the age they usually do that? That way if we have to keep them separate we could possibly put the neutured male with the females so he wouldn't be alone.
Can you put the two males together (again, you are CERTAIN the skinny is male?)? I can't answer that without knowing your pigs. You can certainly try. There is a very good guide on how to do introductions on this site. I would follow that to a T if you want to have good chance that your males could live together. The details are important to follow, and it involves a substantial time commitment from you when you do it (at least several hours) as well as a large, neutral area. Don't fudge on those instructions, especially since your older male is already acting the way he is and he has teenage hormones coursing through his little body.
I would try to introduce them *properly* (as per the instructions) sooner rather than later. Expect some quarreling and posturing. As long as there is no blood or chunks of skin flying about they are fine. It will sound really bad to you, though. As long as it just *sounds* awful you are fine. Also, what seems like cowering and squealing to us could just be guinea pig posturing for "I accept you as dominant" and doesn't necessarily mean "I'm scared."
As for neutering, you should probably only neuter if the boys will be living with girls. Neutering does NOTHING to inhibit sex drive or personality, so it won't make them less aggressive with each other. It is risky and I would NOT let a vet neuter my male unless he has done a *lot* of successful guinea pig neuters. Complications are easy to come by, even with a good, experienced vet.
That said, there *are* some side advantages to neutering. We neutered ours at 5 or 6 months old (before he was full grown) and he never grew as large as intact males get. He is now full grown and is the exact same size as our full grown intact females. (Intact males will grow a lot larger than females.) This makes life together with the girls a lot nicer.
Also an advantage is that he will no longer have a "sac" to drag along the ground, which means he won't be getting "stuff" (like hay and bedding bits) up in his anal cavity. Intact males have to be cleaned out every once in a while (once a month at least, I think). It's not hard (I've done it), but it's not fun either. It involves using a Q-tip and some mineral oil and swabbing out his anal cavity until the swab comes out clean. Depending on how much gunk is in there, it can take awhile.
Since our male was neutered we haven't had to clean him out at all in over 2 years. So that's kind of nice to not have to do.
Neutered males can still "do it" when the females will let them, you just won't have babies. This is also why you can't have more than one neutered male in with females, because the males will still fight over them all the time.
If you neuter one of the males because he won't live with the other male, then do so before he gets full grown so he doesn't get bigger than his female herd mates.
He will still need to be kept separate from any females for about 3 to 4 weeks after the surgery. This is because guinea pig sperm is probably the heartiest stuff on the planet. It can live in the "ductwork" for that long and he could still impregnate any female he was put with for that long after the surgery.