We would prefer printing the receipts on a custom paper size does SchoolAdmin Support it?

Yes. In SchoolAdmin you can print receipts on A4, Half of A4 size (A5) and 1/4th of A4 size (A6) and any other size. you can open the receipt template in Open Office and change the paper size and formating.

Our receipt headers will have different headings for group of fees, is it possible to configure in SchoolAdmin?

Yes. You can. For example, For Management fees you can give receipts in the name of your Trust / Foundation and For the School fees you can collect in the Name of your School.

We want different receipt numbers for different groups of Fees which are collected is it supported?

Yes. You can have different receipt counters for every group of fees that you collect. There are many options available in the software.