I use empty spaces in the dock to group applications in the dock. My dock looks like this:
Screen Shot 2015-07-28 at 20.07.46

To add an empty space, open the Terminal and type in

defaults write com.apple.dock persistent-apps -array-add '{"tile-type"="spacer-tile";}'
killall Dock

You can drag and drop an empty space like application icons. To remove it, drag it from the dock.