Hi kbquinn,
From what i can see, with some quick testing, we can sync over an Alternative Contacts "name" field for each Customer, but only if when adding this to Quickbooks, you use the contact type as "Secondary Contact". However, this appears to be the only field from this area that will get synced over if you take this approach. If you require these alternate/secondary contacts additional details you would have to add them manually to Method.
May I ask why this has come up, have you been using this area in Quickbooks for alternative contacts? Method has the ability to add more than one contact per Customer, even though the contacts can't get pushed over to QuickBooks, you can add all of their contact details here and keep it organized under each Customer. Would it work for you to use Method to store the alternative contacts?
-Ben