The Criteria sets in Importacular allow you to match the data in your data source (or file) to the data in the Raiser's Edge. To use the Criteria sets to identify records, you will need to map enough data to identify your constituents (you may also need to map additional fields if you will also be creating new constituents).
You can then use the functionality to create a query of new/existing constituents to isolate the records in your data source. Unless you change the sort of the query, this query will be sorted in the same order as your data source.
You can add the Constituent ID and any other information that you need to the output of the query you've created and work with it as needed.
A video tutorial to demonstrate this process can be found using this link.