Offline payment entry for students

Hi

I’m trying to create a ledger entry for a student who has paid to college.
In the current set up of frappe, it goes through a cycle of payment link → student received an email → paid–> ledger entry is made.

But in our case, it happens offline wherein student deposit to college account directly.

To resolve this I have introduced a filed to bypass the entire process due to which GL entry amount is doubling.

Can someone help what is the ideal solution for our scenario or solution to the said issue.

Thank you
Chinmay