That sounds very similar to my situation. I enter both my kids in the dependent section (under Personal Info). TurboTax asks the right questions that pertain to a two household situation: which parent is claiming each child and how long they lived with you. The system knows how to handle two parent households (and does it very well, if you ask me!).
If you are claiming the childcare expenes for both kids, TurboTax will let you know if you can claim the expenses for the child you don't claim as a dependent. If you can claim those expenses, make sure your ex isn't also claiming them - your return will get rejected. That happened to me this year. Only one parent with more than 50% custody can claim these expenses.
I'll attach some screenshots below to give you an idea of how it works. It's really easy to follow.
