Assuming you have installed PDT, you have a few choices for how to update it to a newer version.
Bear in mind that you cannot update from PDT 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 (the first option above) then you can move from 2.0 to 2.1 because the all-in-ones also include the correct version of Eclipse.
Get a New All-In-One
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.
Install Updated Plugins From Remote Update Site
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.
Install Updated Plugins From Archived Update Site
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.
Install Updated Plugins From Runtime or SDK Zip
Shut down Eclipse. 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. Some 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, since newer plugins will have larger versions and therefore be loaded instead. Removing old versions will speed up Eclipse's startup time, though.