As for the second:
When sudoing you cannot use graphical programs, because your screen is not enabled

(sadly I have no clue of Eclipse. Try asking in the ubuntu forums or google for "pdt ubuntu eclipse" or something, sorry)

Have you tried using the update manager built into Eclipse and adding the PDT discovery site to it? Generally speaking, ANY major feature of Eclipse can be found at a discovery site for automatic installation and updating (including Eclipse itself).

- Help -> Software Updates -> Find and Install...
- Search for new features to install.
- New Remote Site...
- http://download.eclipse.org/tools/pdt/updates/ (It's listed right on the PDT download page)

Should install everything automatically for you. And also of note, the installation directory for Eclipse plugins should generally be /opt/eclipse/plugins/ if you need to do a manual installation.

I also strongly recommend using the eclipse upgrade method. It's also worth noting that eclipse 3.3 doesn't seem to like PDT at all and wouldn't run it for me no matter what method I used. eclipse 3.2 worked great though.

Upgrade Instructions

Another method to try is the all-in-one packages.

PDT All-in-One from Zend.

The first set pdt-1.0.0.I20070520_debugger-5.2.6.v20070507-all-in-one-* uses eclipse 3.2 and the second set pdt-1.0.0.S20070611-M1_debugger-5.2.6.v20070507-all-in-one-* uses eclipse 3.3 and doesn't work for me on linux or windows.