Your problem is not directly linked to the new Eclipse Installer.

A P2 Update site (this is also more or less what you bundle pool is) consists of folders (plugins
, features
…) containing jars and/or bin files and some XML Files named artifacts.xml
and content.xml
(sometimes those files are also packed in jar
files).
The XML Files keep a record of the available plugins. You cannot add something manually without tampering your pool.
You should install additional plugins with the “Install new software…” of Eclipse. If you like to automate this installation process for each of your installations (or inside a team), you can work with the Oomph setup file to do it.