Am I overlooking something silly or do I need to enter my key everytime I point to a new workspace?
Eclipse doesn’t provide any mechanism for installing a “global preference” or something like that. That’s why you also have to go reinput all your preference settings when you create a new workspace. The subscription key is just one such setting. To make this easier, however, Eclipse does provide a preference export/import mechansim that will duplicate all your preferences, subscription key included. You can get to it at Window > Preferences > Export… at the bottom of the window.
Also can’t I run two instances of myEclipse on the same machine?
That one you can find here:
http://www.myeclipseide.com/PNphpBB2+file-viewtopic-t-2828-highlight-subscription+two.html