Attempting to setup a multiple server file share. I am really not sure how to configure and setup the headless system for sharing? Seems easy enough with the webapp and have my windows system appear to be working not sure how to get my Linux headless systems to sync up as well any help would be greatly appreciated.
It's not really clear from that what you want this server (or servers?) to do.
I think if you explain some more we can help better.
I guess you have a repository on Windows using the webapp and you want that repository to be synced to one or more servers. The webapp has a dialog to Add a Repository on a Remote server. You'll need to install git-annex on the server, and tell the webapp the password to use to ssh to it, and otherwise that's pretty simple.
That will get you a git repository on the server that will store all the files from your Windows repository. Since it's a bare git repository by default, all you can do with it is clone it to somewhere else, which can then get files from it. That could be another server or another webapp client or whatever, depending on what you're trying to accomplish.