Enter relative local paths (eg /server/myfiles) and absolute GitHub paths (eg https://github.com/user/repo or https://github.com/user/repo/tree/branch for branches), as per the examples. With this done you have established the source paths at both locations, as a pair.
You can then choose a path pair and this then becomes your new root path in ICEcoder.
The file manager then displays a new GitHub icon, which you can click on to perform and show a diff check between the 2 sources. These diffs can then be committed and pushed to the remote path at GitHub or cloned to your local path, to sync your files.
If you want to set another root path, this can be done in the Help > Settings screen.