All! This may be a silly question, but I have to ask so

Hi All!

This may be a silly question, but I have to ask so bear with me....

I have a Multisite that clones a copy of my main site upon subscription.
If someone decides to become an affiliate and a referral subscribes via their site , does the Affiliate plugin credit them for the impending sale?
In other words are referrals only rewarded via the link provided by the Affiliate plugin?
If yes, is there a way to have the above scenario hold true?

Thanks,

Mike