You can not mark the lines that are paid, in QB the whole invoice is considered one amount, and you receive full or partial payments on that.

In reporting though it changes, if you are accrual based then the sale income is posted when you save the invoice

in cash based reporting, QB will allocate a portion of the partial payment per item line on the invoice and for sales tax, you have no options as to how QB does the allocation and it only shows up on cash based reports