Subscription Center options/email program unsubscribes

I have a working subscription center with opt-ins on a form setting boolean values (Webinar T/F, Newsletter T/F...). Each email program has a filter with the specific opt-in type of message going out set as true. The subscription management page has the 5 opt ins and three buttons (subscribe to all, suspend, and unsubscribe from all). All of these are controlled with smart campaigns setting the opt-in , marketing suspended, and unsubscribed booleans. However, when we run a batch email and someone unsubscribes, the unsubscribe metric in the dashboard is not reflecting the change. Their lead information shows unsubscribed but the email dashboard stays at 0% for unsubscribes. In admin I have changed the default unsubscribe anchor to the new management landing page:  href="%mkt_opt_out_prefix%Subscription-Preferences.html?mkt_unsubscribe=1&mkt_tok=##MKT_TOK##"

My question is how can I set it so if any opt-in boolean is changed to false, the email program will reflect an unsubscribe even though it is not changing the systems "unsubscribed" value? If that is not possible, I'd at least like to get the systems unsubscribe to attribute the change to the specific email program it came from.

This is the best information I've found on the subject but still unable to figure out how Marketo attributes unsubscribes in email programs. I've heard to delete {{system.unsubscribeLink}}, show it with a line height of 0 (hidden), and a bunch of others. I'd like to get more information on how Marketo actually uses this token and the unsubscribe system as a whole before testing.

Any information would be greatly appreciated! Also, if I need to clarify or post code just let me know.