What a coincidence - I just finished our troop's treasurer report.
No, you should not be running a deficit. Are you factoring in other assets that will be coming in, such as payments that haven't been made yet for campouts, etc.? I tally assets (checking account, council account balance, payments yet to be made, etc.) and tally encumbrances (scout account totals, outgoing payments in the near future, etc.). Your assets should be more than your encumbrances.