Some PC-style keyboards only have one Windows key, with the right-hand equivalent being the Application key. So you only get one command key in OS X.

Fortunately, you can use Karabiner (https://pqrs.org/osx/karabiner/ - formerly known as KeyRemap4Macbook) to turn the application key into another copy of the command key.

Took the words out of my mouth. You've gotta teach yourself to do this on a split keyboard.