If you are using the authorize.net gateway & experiencing some discrepancy with deposits, it's important you verify your authorize.net cut off time. This is when authorize.net is passing your total sales to the processor to batch out.
If the cut off time is before your restaurant closing time, this will cause issues.
Read more about it here https://support.authorize.net/s/article/When-Are-Transactions-Batched-for-Settlement-and-Can-This-Time-Be-Changed