Ooh, a shared carrier sounds like a good idea then!! I honestly think you'll be fine. I think they're more curious / into exploring when they're younger. I hope they do well.
You seem to have a lot of good replies, but I popped in here and figured I'd add my two cents. I've moved around a lot since getting my cat, at least half a dozen apartments over 5.5 years. She's always pretty freaked at first in a new place, but she bounces back eventually. As far as going back and forth between places, when I lived in New York I visited my parents' house in Jersey a lot, and while she's nervous around my parents, she loved having two homes (especially because a house in the suburbs gives A LOT more room to explore than a Manhattan studio). I think especially because you have the two that will have each other, they'll adapt and be okay, I would just suggest making sure they know and are used to your SO before they stay there.
I wouldn't worry about not being seen as mommy. My cat was a stray initially found by my now-ex, who had her for about two months before I took over. We were long distance, but my cat still was in love every visit, and honestly knowing that is one of the roughest parts of the breakup because I feel bad.
When kittens are that young, they're pretty adaptable, so you're in luck there! My three cats and I have moved three times in two years, but we've made it work. I think the most important thing is moving all their stuff with them. In particular, I find it helps to have several blankets/towels that have the cats' scent all over them, which you can then put all over the couch/bed/floor at their "new" home. They'll feel more comfortable if a new environment already smells like them. Also, as someone mentioned earlier, it can help to keep them confined to just one room for the first few days; though very young guys like yours are usually adventurous, if they grow more timid as they get older, establishing one room as a "base camp" of sorts that they know is safe and smells like them can help give them confidence once they start to explore the rest of their new space.