You click on the emblem and there should be an option to spend. If you have not spent it to get the skill yet, then it will be destroyed and unlock the skill. If you have already spent one before, then it will simply speed up what you're already learning.
click on the token, and press the 'spend' option. The magic rock will then ask you if you want to spend towards learning the skill. Make sure you're spending towards the skill and not towards favor:)