Support for subdomain matching

We have a site that tracks affiliate sales by utilizing subdoamins but it doesn’t appear that the custom settings carry over to the duplicated subdomain sites.

For example: affiliate.mysite.com is just a mirror of mysite.com. I have globally disabled some plugins, then manually turned them on when needed. The problem is the site with the subdomain prefix doesn’t recognize the plugins manually turned back on.

Is this possible? If not, can it be contracted out?