I've never tried the "Projects" feature of github, I didn't even know about it. If John says it's more cumbersome than labels and milestones, I believe him, but you may wnat to try the "Projects" feature as well and judge for yourself.
Since you're not the Eclipse project committer, you don't have permissions to create labels and milestones.
In that case, I suggest creating an issue in the github repository in which you'd like to create labels and milestones and specify what you'd like to have. Anybody from the project committers can do that for you and I believe that at least some of them would get a notification about your issue and will react. I say that because I usually turn off notifications for repositories I'm not actually interested in to avoid flooding my mailbox. If nobody reacts, the next step would be to ask on the mailing list and point to the issue you need to get solved.
--Ondro