"When I enter the donations by Donation (Sales Receipt), what is the" item" for? and what is that? why not the chart of account?'
Items control the flow of the data to the accounts and allow for Better tracking and reporting.
Example: You collections include Hurricane Relief Donations. That Service Item links to your regular Restricted Income account, but you use that item for the Donation receipts and for the Giving, and now you can report on Hurricane Relief specifically, as Item-based reports. The Accounting is not micro-managed for various Missions and purposes, in other words.
"how to record the deposit in QB after we deposit the cash+checks to the bank"
You do this After the following:
"how to enter the donations received every Sunday at church?"
You track the giving, and then you address the Various destinations of funds. That means you can Summarize the day on one sales receipt, like this:
Or you want to track it Per Donor Name, for meeting your specific requirements for reporting.
Or, some of each.