OK, I read that as you worked something like 6-2, and he worked 2-10, removing the need for childcare. If you both work days, its totally doable.
If he's only away for a fortnight at a time, thats likely to be a sunday travel, the weekend in the middle, and possibly the Sat at the other end. 6 times a year. You could probably arrange for your parents to come and visit for some of those trips away. Or you could go visit them for the weekend?
You just get on with it. Yes, it can be a bit relentless if the kids are ill. If you are ill, you have a slob weekend, where everyone snuggles on the sofa watching films!!!!! BUT, for 6 weekends a year? The chances of someone being ill are fairly slim.
In some ways, it can be easier. Kids and I are totally happy with pasta every night. DH would want more variety, and some meat. So evening meals are simpler. I eat with them (now they are bigger, we all eat together at 5pm whether DH is here or not). Yes, I don't get any time out of the house without kids, unless I put in a half day holiday. You would be on ML when this starts, I guess? Which in some ways makes it easier - you could go with him if he was going somewhere that would work, or you can go to your parents. However, it is pretty relentless with a small baby. Ours are 3 and 5 now, and its fine - they are big enough to set of on playdoh/colouring/cars and achieve something. So I would imagine the second year would be the toughest - back at work, with and under 2.
Once you get to the point of fairly predictable kids to bed at 7, and thats it for most of the night, and thats when you get your break. and control of the TV viewing
Also, for two weeks, some things just don't happen. Don't change the sheets, don't sweat it. There is less laundry (til he gets back), and you can do what YOU want to do with the kids the whole time. It can be quite refreshing.
You mention DH is unhappy where he is at the moment, and if this is a good step, I'd say go for it. If its a disaster, he can always start looking for something else.