I'm updating a site that has designer disabled, but I need to make changes to the master page. I would prefer to upload a new master page and apply that. I can upload it, but I can't find an option in site settings to allow me to apply it to a page? Am I missing some permissions?
Enabling the Publishing features on the site collection and site will give you the page on Site Settings to set the master page.
I think that in 2010 you could still navigate to this url
http://spserver/sites/thesite/_layouts/ChangeSiteMasterPage.aspx and change the masterpage even on non-publishing sites. In 2013 AFAIK this is no longer possible