Hi mholden,
Leads are actually stored in the Customer table, which in turn is just a view of the Entity table. The entity table stores all customers, leads, employees and vendors. The only difference between a lead and a customer is that a lead has a value of Yes in the IsLeadStatusOnly field. When you convert a lead to a customer, Method simply changes this value to No and tells the sync to push the record to QuickBooks. Since there is no copying of data to another table, the data in the custom field that you have added will remain the same. I hope this helps.
-Audisho