Affiliate tracking number to cover whole site

Hello,

I' m running several multistores and se have sales people under every Shop. Sales people and us split comission 75%/25% each store item.

Is there' a way to add affiliate tracking codes to f.ex index.php so these comission rates would automatkailu forwarded to everyones affi account? Se would like to get off rid of direct affi urls.

Also is there's a way to use same affi tracking code for multiple affiliate to do comission split?