I think both suggestions address only part of the question. By far the easiest thing to do is create different payslip earnings items for different funders. These can be defined to post the employee’s earnings to different expense accounts for work on the different grants. They will still post the liability to Employee clearing account. This resolves keeping track of where the expense for employees is posted.
The second issue is paying the employee to clear the liability from Employee clearing account. If you are actually using separate bank accounts for different grants, you have no choice but to enter multiple payments, because Funder 1’s money is in one bank account and Funder 2’s in another. There are two ways around that, if you want to pay only a single payment each payroll period:
- Open a payroll bank account. Transfer funds from the funders’ bank accounts to the payroll account each payroll period in the amount necessary. Many businesses have bank accounts used only for payroll, especially if they use an outside payroll processor. (You could also use your current bank account for this function—same thing.)
- Deposit all your grants into a common account and make all payments from there. You would need to structure you chart of accounts to enable you to know how much of that account belonged to each funder. You might do this via equity accounts. I recommend consulting a qualified local accountant with expertise in charitable accounting, as rules vary from jurisdiction to jurisdiction.