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You can record multiple payments against a single bill in QuickBooks Online by selecting Make payment > on the Bill payment screen, enter the partial amount in the Amount field and save.
If you have multiple bills (invoices) to tie together in one or more bulk payments, enter the bills and then select + New transaction > Pay bills.
On the Pay bills screen, select the date and bank account that the payment was made from, then tick all bills that apply. Check that the total payment amount matches that amount showing on your bank statement before saving.
For further information on managing bill payments in QuickBooks Online, see our Community guide.