Import Transactions will look upon a matching deal with the same Collector and Merchant Number.  These can be set on the deal tracking page as the screenshot below shows:

The Collector must be a company in the system with a contact type of 'Collector'.  The same merchant number can be re-used and if it this happen, the import will upload to the earliest funded deal that has not been paid off.  If all are paid off it will apply to the latest funded deal.

Merchant numbers are alphanumeric and were originally designed for the number provided by banks.  If the bank does not provide a number you can use your own.  A common example of merchant numbers customers use is the deal name.