When paying the deposit manually e.g. the registrant sends a cheque and I enter £40, should this come off the total amount to pay? If yes, it doesn't appear in the Gross Amount field? So, £250 - £15 (member) - £40 deposit = £195
I have saved the record after I have said Deposit Paid.

The gross amount is the total payment amount which users have to pay for the registration. It won't be changed when you mark paid for deposit amount.