I would recommend transporting them in separate containers, too. 1 hour is a lot of time for birds that don't know each other. I think two would be fine in the pet carrier, the rest in the cage, if you have the room to fit both into your vehicle.
Once you get home, if you don't have any other chickens, I think it should be fine to put both groups together, assuming you have enough room in your setup for them to avoid each other and not be in each other's personal space. So a spacious coop and run that meet at least the minimum requirements for space - 4 square feet of floor space per bird in the coop, and at least 10 in the run. Ideally you'd have more, since you're integrating, and the first few weeks might be dramatic as the two groups get used to each other. You are better positioned for success integrating, with 2 new groups, compared to introducing 1 new group into an existing flock, because both groups will be new to the territory. Nobody can claim it as theirs and defend it from the others. So they will have the shared challenge of being new, and will be on an even playing field. The 4 will have a numbers advantage over the 2, but temperaments will play a role, too, so what pecking order they establish is anyone's guess.
I don't think quarantining the two groups away from each other would be practical in this case. They'll be riding in the same vehicle for 1 hour, so that already breaks quarantine protocol. Once there, you'd need two complete setups (coop/run) that are very far away from each other, with separate tools and supplies, and either separate caretakers or for you to change clothes/shoes between visits to both. Which is not practical unless you live on a farm with lots of space. I'd recommend inspecting each bird carefully before you release it into the coop/run, just so you can catch anything obvious like mites, scaly leg, etc. that would need treatment to prevent spreading it to the others (if they haven't yet).