If I have 20,000 to put down on a 220,000 home, how do I make it clear that I want the closing cost to come out of the 20,000, or can you not do this?

Let your lender know how to distribute monies for closing costs/down payment and your lender will coordinate with the closing or escrow company.

Ditto. Or you could negotiate a seller concession to pay all or some of your closing costs. Then more will go towards your downpayment and possibly put you into a lower rate. Conversely it may be a wash due to price inflation to cover closing costs.