Sometimes the best way to organize your systems is to tweak the settings to simplify the configuration. Macworld has some tips for some OSX system settings to make your Mac work better. Examples:
To get the most value out of your software investment it is sometimes worthwhile to do a quick tour of the settings to see if you can optimize them to better support your work flows.
Every once in a while check the items you have in the menuBar to confirm they are all being used regularly. You may want to remove them if they aren’t something you use often.
Scan through your applications periodically to see if there are any that should be deleted.
Getting rid of visual and mental clutter will help you focus and avoid wasting time on items you aren’t getting value from.