To make a user a site owner in Google Webmaster Tools, you must verify the user as an owner. (Good luck finding that in the documentation.)
By Matthew Malinowski, 2013-04-25
If you care about your site's position in Google results, it's a pretty good idea to have it set up in Google Webmaster Tools so you can keep an eye on various results-related statistics. Webmaster Tools also does very basic problem detection -- if a part of your site becomes nonresponsive, Webmaster Tools will report that to you.
Google Webmaster Tools has user classes: Restricted, User, and Owner. You can tell you are not an Owner when you click "Manage Site" next to your site at https://www.google.com/webmasters/tools/home, and you don't see "Add or remove users" in the menu. (You also won't have access to "Users" or "Associates" under Configuration in the site's sidenav.)
To make your non-Owner account into an Owner, you need to verify your ownership. Go to https://www.google.com/webmasters/verification/, you won't see your target site in the list there. Click "Add a Site", and enter the domain for your target site. Before you do a verification step, click "Verify" -- it might just work if you are a verified owner of a subdomain of this site. Otherwise, do one of the verification steps, come back, click "Verify", and you'll be a verified owner.