Run this from your terminal to execute the setup script. It creates the directory and downloads the template right into this new folder.
curl -s https://gist.githubusercontent.com/DivineDominion/ab1abe8d2b93d4b73d69/raw/6a7066f1fbcf45e3c47a8d85acee475dd33bd32c/install.sh | bash
Aferwards, you can change the base directory in ~/Library/Application\ Support/nvALT/template.html
as expected.