Can someone here give me an idea how should I make
a transaction form or should we say a payment form.

I already have a database with lists of students in it.
Also a database with an event in it. Along with a fee on which every
student should pay.

The problem is I want to make a form on which if this entry(student)
were to make a payment his/her name will be marked as paid in the student database.
More like a payroll system.

Sorry I am kinda noob when it comes to equations or money matters in Vb.net
All I know is add edit delete and search. Can somebody point me to a tutorial
or a good idea where to begin?

You can use what i call in my own term, 'trackers'. Its a simple status identifier to me. SO maybe u can have another column in your table that checks the status of payment per student basis.... At least, that's a start for starters.