To use git-reflow with a GitHub Enterprise account, there are some additional switches available to the git-reflow setup command. You should be able to use git-reflow for both your Enterprise and non-Enterprise repositories. Because of this, there are a few scenarios that may apply to your usage of git-reflow:

You use a GitHub Enterprise account for the majority of your repositories:

$ git reflow setup --enterprise

After this, anytime you want to use GitReflow with project that uses a regular GitHub account:

cd replace_with_your_non_enterprise_project_path
git reflow setup --local

This will setup your project's git config with the OAuth token generated from the credentials you provide.

If you only use GitHub Enterprise for a select few repositories, you'll first want to setup GitReflow as normal:

git reflow setup

Then for your Enterprise projects, you have to setup GitReflow for each one:

cd replace_with_your_enterprise_project_path
git reflow setup --enterprise --local