Very similar to happyauditor, annually, we develop our audit plan based on risk assessments and rotation schedules, and budget the hours for each audit, I estimate time for special projects, and budget for admin time, vacations, holidays, training, etc. I then compare the total hours to the number of staff and their available hours (e.g. 2250 hours per auditor).
Next, I schedule out the audits by quarter by auditor. We maintain time schedules daily and input them into a spreadsheet monthly (or more frequently if necessary). I use this to determine where we are compared to budget.
I report actual hours to budget to the Audit Committee quarterly and if we get off track, we work more overtime and/or I recommend amending our audit plan or outsourcing some audits depending on risk assessments, needs from external auditors, and expectations of examiners. Hope this helps.