You have a few options.
a) Each time a new, updated all-in-one is made available, download it, unpack it, and point it at your existing workspace. Simple, self-contained, and no updating required. (Note that anything else you've installed into your Eclipse, like for debugging or other scripting support, will need to be reinstalled.)
b) From an existing installed all-in-one, load up the update site you like best (interim, milestones, or releases -- see http://www.eclipse.org/pdt/updates/ for the list) and install updates into your existing Eclipse. Restart when prompted.
c) Download a new, updated Update site zip. Unpack it. From an existing installed all-in-one, use the Install Manager to install the new plugins from the unpacked local update site. Restart when prompted.
d) Download a new, updated SDK or runtime zip. Unpack it into your existing Eclipse's dropins folder, eg., ~/eclipse/dropins/. Restart eclipse with the -clean flag, and be prepared to wait a bit as it finds the new dropins and loads them. (The purists might say that you should remove the old stuff in dropins/eclipse/plugins/*pdt* and dropins/eclipse/features/*pdt*, but you don't strictly have to.)
Bear in mind that you cannot update from 2.0.0 to 2.1.0, but you can move from 2.0.0 to 2.0.x. This is because 2.1.0 requires Eclipse 3.5, whereas 2.0.x require Eclipse 3.4. If you're simply replacing one all-in-one with another (option (a)) then you can move from 2.0 to 2.1 because the all-in-ones also include the correct version of Eclipse.