If more than one unit is linked to the same member, the system treats these as linked units. When entering payment, if more than one unit is shown, it is not mandatory to put the payment against both units. You can choose to put appropriate payment amount only against charges of one unit and then the payment would be treated against only that unit.
If you want, you can put the payment against charges of more than one unit and then the payment would be against more than one unit.