Marketpress and affiliate plugins

Hi,
I am trying to set up a way to charge a fee for an application on sub-domains. There will be different fees on each site but I want to charge a $50 fee per application that goes to the referrer (me) instead of percentage. The sub-site would get the majority of the fee ranging from $75-$200. According to the support page, I could add the code to my functions.php and use 50.00? Do I need to add both groups of code below?
$amount = apply_filters('affiliate_click_amount_filter', '0.00', $affiliate );

add_filter('affiliate_click_amount_filter', 'my_affiliate_click_amount_filter', 10, 2);
function my_affiliate_click_amount_filter($amount, $affiliate) {
$amount = "50.00"; return $amount;
}
Do you have any suggestions on the best way to set up marketpress with affiliate plugin with multi-site? I am not sure if the best way would be create an application fee as a product on each site or all application with fees on my main site. If I do it the latter I don't think I could refer as the affiliate, right? Or maybe an external link on the main site back to the sub if I want to use both?
Thanks,
Jeremy