I just noticed that you haven't had a response to this yet (6 days after posting). Do you still have questions/need help?
To answer a few of your questions, just in case, give mom unlimited food. A few oats also provided mom with the energy she needs.
As far as cleaning/bedding is concerned, when my degus gave birth, I didn't disturb the nest until the babies were fully mobile. I only spot-cleaned the cage and kept providing them with paper towels so that they could replenish the nest. The moms kicked out dirty litter, which I then could grab and throw out.
I have heard of people marking babies with markers, but I wouldn't recommend that. The babies need to be at least 6 weeks old before they can be separated from Mom. When they reach that age, and before 8 weeks of age, separate the male babies from the female babies. Any prospective adopter can then decide on whether they want males or females.
I have two litters of babies – each mom and her daughters have their own four-level cage, and dad is in a third four-level cage with his sons. I can't tell everyone apart other than those that have had issues or have distinctive ear injuries, or extreme personalities.