You can clone the Arduino-Boards repo to ~/Arduino/hardware/keyboardio/avr, like this:
git clone --recurse-submodules https://github.com/keyboardio/Arduino-Boards \
~/Arduino/hardware/keyboardio/avr
This will pull all the latest plugins and whatnot. I’d recommend backing up ~/Arduino/hardware first, just in case. (And it should be moved away before doing the git clone, so git won’t complain.)
With the plugins installed (either installing the board manager via the IDE, or doing a git clone of Arduino-Boards like above will install the official plugins), you can just #include "Kaleidoscope-OneShot.h" and follow the examples in its README or its example sketch. There’s no additional thing to install.
To make modifications to your keymap, I suggest forking the Model01-Firmware repository, and committing any changes you make to your own fork. That makes it easier to pull in changes, should you want to. Not to mention that having one’s keymap under version control is very useful. 
As for setting up your own LED effect, that can be either easy or challenging, depending on what you want. We’ll be happy to help here on the forums should you need assistance with it!