You need to create the folder foo with a folder called plugin and then foo.vim inside it -> foo/plugin/foo.vim
" Also say a plugin has syntax files and an ftplugin folder then do I just drop the plugin in pathogen and it is supposed to work?
Yep. Normally vim plugins are shipped in zip files that contain the structure and are meant to be installed on top of your .vim directory. All you do is instead install them into .bundles/pluginName instead. Also, since a lot of vim plugins are kept in source control anyways, a lot on github, you can simply use git submodules to version your plugins as well making updating them a cinch.