Unless your state mandates it (e.g. Massachusetts) or your policy includes savings accounts in you funds availability schedule, generally savings accounts are not subject to Reg CC hold requirements so you can hold as much of the deposit as you want on the savings account and then provide $5,525 available on the next business day on the checking account.
If both accounts are subject to your funds availability schedule, Reg CC does not mandate how the available funds re broken down by account provided that the total amount available on the first business day totals $5,525. How you split it is up to you and perhaps with some input from your customer based on which account they may need to access in the short term.