This a noob alike question, but here we go. I´ve read about Twitter Bootstrap (among other presentation frameworks), which gives the designer/programmer the tools to build easil
as ebaxt said, Bootstrap is only a modular front end technology. Your question is about the visual part of a Java EE based application.
It will basically deal with MVC patterns and their implementation/technologies (EJB, Spring MVC).
And then you will finally deal with presentation technologies : writting in .jsp pages, using JSF or Struts or GWT technologies or (of course) BootStrap (like any other js and css code) to get visual results and accessibility. By doing this, you will get an entire well structured app.
Sorry for English mistakes if I have done some, I'm a french guy.