Questions about 1099 and refund?

Yup, you're right, he'll have to pay them all at once when he files. Yes he must still file , can claim the kids and maybe you, and be eligible for the usual credits. If he's entitled to any credits, they'll apply to the tax he owes. Whether the credits would cover what he owes or not, and still maybe give a refund, depends on how much he made for the year. If you'll post again with that info, somebody can probably give you an estimate.