I was wondering if there is a plugin for Eclipse that allows the user to build a version of the project/application that is packaged in a .deb?
If possible to be able to modify the configurations before building it.
There is no plugin that does this. This is because Eclipse has never been made for that purpose, and therefore does not include all the particulars of Ubuntu Packaging. Any plugin that might do this would be sketchy at best, and would probably screw up the package in a manner that violates Debian packaging.
(Ubuntu is based off of Debian, and uses Debian .deb package formats :P)