I'm still on Quicken 2005.
I know of no good way to record a deposit of multiple checks. The split entry doesn't have enough fields to indicate both payee and memo information. But there is no way to match with the download of the deposit except by splits. I even tried making multiple entries and then doing a manual match, but it converted all the entries to a single one with split catagory and put the payee's into the memo field.
Is the situation improved in newer versions?