Tracking IDs/Sub IDs can be used for many reasons, including tracking campaigns, websites, or even individual users.
When an affiliate network offers sub ID tracking an affiliate can choose to pass custom information to the affiliate network's tracking system.
When a sale occurs on the merchant's website the custom information that has been passed via the sub ID tracking parameter in the affiliate link will then be reported in the affiliate network's sales reports.
This way an affiliate can track which campaign, website, or user referred the sale.
The use of Tracking IDs is completely optional and does not affect tracking of your commission or sales.