Invoicing govenment and private institutions for financial aid

Hi
First all Canadian financial aid operates very differently from US Aid.
Some provinces and organizational scholarships require us to invoice them or the funds come in by cheque.
We are finding it difficult to invoice in our main accounting system and then disperse the aid in Populi.
It would save me so much time if we could invoice the organization providing the aid. We are currently having to come up with a convoluted journal entry trail to bring the funds into the bank through the main accounting system and at the same time keep the financial aid liability account balanced in Populi and the funds applied to student account properly.
Thanks
Dennis