First create both units. Then put the tenant in one of the units and set up the recurring charges for that unit. Then from the Property List, Drag the Tenant with your mouse to the additional unit. A wizard box will pop up to ask you all of the questions to get it set up correctly. Basically you are going to copy or move this tenant to an additional unit.
Once you have moved or copied the tenant to the new unit, you will see in his/her Lease/Moving Dates folder that you can click on the first address and fill in the information and click on the second address and fill in the information for that second address. The Recurring Charges folder is also going to separate the charges for each unit. If you click the New button on the Recurring Charges folder you will have a chance to select which unit the charges will be associated with.
Once all of the recurring charges are set up, if you go to the Income form and see the actual current charges listed you will see the unit number in the memo field of each charge. When the tenant makes a payment you can apply it to one or all of the charges. The statements and reports will all reflect the charges and income for the appropriate unit.