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.
HTH,
Nick