The company fiscal year and the personal income tax year (which the current YTD values are based one) are often two completely different things.
We will eventually add this feature, but I don't think it will do what you really want.
The problem for us is that our company sometimes provides large payroll advances that are deducted from the employees timesheets.. sometimes over the entire fiscal year. The paystub generated by TimeTrex shows how much was deducted, and also a total deducted under YTD. When January 1st rolls around, that employees year to date is reset to $0.00
How are you deducting this large advance?
YTD values for accrual pay stub accounts don't get reset ever, so if you add this large advance to an accrual account, then deduct a few hundred dollars/month from it, it allows you to easily keep track of the balance owing without it getting reset at the end of the calendar year. The amount deducted will get reset which helps for the employees tax purposes, but not the overall accrual balance.
We are planning to add a feature that will automatically pay out, or add to an accrual account until the accrual reaches a specified balance, such as $0 or $1000. This should help you further in handling large advances/loans.