Seems your accounting has been needlessly tangled up for contract or grant. Have you been audited yet? 

These are three different components:

Fund

Object

Project

Mixing all into an account number does not do any proper calculations needed for billing or reporting.

Account

- Salaries

- Leave

- Fringe

- Indirect Cost

- Supplies

These are completely different elements of accounting for project or grant and computed differently.  

I strongly suggest hire an experienced person to assist you with getting setup properly to avoid audit issues.

I have done this work for 3 decades and there are plenty of experienced people who can assist you on this.