As of the current 10.0.0.8 version, you have to "enable" a project for codecover and declare which types of measure you want to use, before you the measurement will work. Nevertheless, you can check "use for coverage management" on classes or packages for non-codecover-enabled projects.
IMHO this is a usability flow, which tends to confuse new users. Here's my proposal: After checking "use for coverage management" in a not yet codecover enabled project, codecover should open up a wizard/popup and inform the user, that this project is not yet enabled for codecover. It should offer the user the option to enable it, together with the possible measurements available - just like in the current dialog under properties. I think this should enable a vast majority of users to advantage of codecover, without reading the start-up manual.