Can I allocate invoiced income to different funds and categories?
When creating invoices you can choose to allocate the income to as many different funds and categories as you like. It does not matter how many income allocation 'line items' you include on the invoice.
Scroll to the bottom of the 'Create Invoice' screen. Within the Income Allocation section, use the drop-down menus to select the funds and then the income categories you need. To add a new line, ensure Income Allocation is set to 'Allocate Manually', then click the 'Duplicate line' button on the right-hand side.

Note: Once the invoice is created, if you create accounts on an accruals basis AND you have auto-accruals enabled, then a separate 'Accounts Receivable' record will be created for each fund.
To help you better understand the invoicing module as a whole, please visit the module overview page here.