A project in intellij consists of modules. Modules can be java modules, or android modules or whatever. Modules contain your java code and all that stuff. A Module can reference a library which can be a project library or a global library. Global libraries have to be defined only once. Project library in every project you need them.
Packages are a java concept and are IDE independent.
Lets say I wanna do a little game. I would create a intellij Project called “mySuperGame”. Then I would create two java modules from intellij, called “logic” and “ui”. In the module settings of “ui” I would specify a project library to use opengl and a dep. to “logic”. The package name of my logic classes would be “com.mysupergame.logic.XXX”.
See http://confluence.jetbrains.com/display/IDEADEV/Structure+of+IntelliJ+IDEA+Project for more information.