Alternate Keys which were introduced with CRM 2015 Update 1, gave us the ability to Upsert and Update records, by defining one or more fields as Alternate Key and use that field(s) instead of relying only on Primary Key.
Alternate Keys can also be used for setting or updating the lookup instead of GUID.
CDS\CRM Destination Component in KingswaySoft SSIS Integration Toolkit allows us the option of specifying the Alternate Key for updating the lookup field.
Suppose we have Contact entity with following Alternate Key defined in it

Key1 on field last name Key2 on 2 fields emailaddress1 and last name
Within the CDS/CRM Destination Component Editor for the lookup field, click on ellipsis for the Text Lookup column. Here we have selected parent contact field inside Lead Entity.

Inside Text Lookup Editor, select the option “Choose Target Field(s)”, in lookup method select Alternate Key and we will see both our alternate keys listed there.

Key1 on field lastname

Key 2 on emailaddress 1 and last name

One thing I have observed that it doesn’t list the alternate key if it is defined by using more than 2 fields. Looks like it is by design.
Hope it helps..