Payroll Allocation by Department

I have an interesting dilemma.
I need to be able to allocate a portion of every employee's paycheck to different departments.  Each department is assigned to a funding source, and each employee could be paid by different funding sources during any given pay period depending upon the duties performed.  This applies to both salaried and hourly wage employees.
I have talked this over with NS support (case #572257), and the recommendation of multiple payroll items and/or using JEs doesn't seem like the most "workable" solution in a company with hundreds of employees.  There must be a more streamlined and efficient process.