Eclipse JDT does auto indentation on typing (i.e. it increases indentation after an opening brace and decreases after a closing brace), so there is normally no need to explicitly run auto indentation or auto formatting if you are just writing new code from top to bottom.
You should verify however, that Project -> Context menu -> Properties -> Java Code Style -> Formatter does have an active Formatter profile.
Besides that, the most common used semi automated tool for cleaning up your source in Eclipse is Project -> Context menu -> Properties -> Java Editor -> Save Actions, which is used to trigger formatting and minor code rewritings. I recommend getting used to that one and basically activate all of its possible options.