If the Unique Per Alternate box is unchecked next to the pricing Criteria, the evaluator will only be able to set 1 price for all submissions.
To make a Criterion Unique Per Alternate, you simply check the Unique per Alternate checkbox (as shown below).
When a Criterion is checked as Unique Per Alternate, a different score will be required for each alternate vendor submission.
Unique Per Alternate criteria will be tagged on the main screen like the below screenshot.
For more information about setting up Alternate Submissions click here.