Troubleshooting Budget Reporting

I am approaching the completion of our Annual Budget. While this isn't my first year with the organization (I've been the Treasurer and President in the past), this is the first year I'm Executive Director/a position we established at the end of 2024.

At the same time, we established a payroll account with funds we received from a bequest. That account was established at the same foundation as our Endowment. Both accounts are listed as Restricted Funds.

In January's board meeting, our budget was not approved because we decided it best to remove our restricted funds from our operations budget. But, that left us at a deficit. Our bookkeeper said that it isn't possible to show allocated funds as an income line item in our budget, but we've since learned that it's completely possible by simply 'tying' the two budgets together with a board motion. The board motion is easy, but I would love advice and guidance on how to establish this new budget format/approach.