If you are planning on reintroducing them after the joeys are weaned, I hope dad is already neutered by now. I would NOT have their cages within touching distance - at least 8-10" apart so they can see/smell each other but not hurt one another. ESpecially when the joeys get to the age they're able to climb around, that could end poorly.
Yes, keep their routine the same as long as they do not seem stressed by it. If they're comfortable with you handling them, then do so. If it seems to bother them, then back off. With the lone one, you will likely be babysitting the joey for her so she can eat. She may need you to offer her food by the pouch if she is not wanting to leave when she gets super big...