This is pretty simple but a bit confusing at first if you aren't sure about how to use this site..
so for anyone who is having trouble with this.. here ya' go. :]

Step I: On the top right of the page you'll see "Friends" and your name next to it..
Click on your name and click on "Dashboard"

Step II: Click on the "Characters" tab.

Step III: Click on "Add Character to Guildwork"

Step IV: Type in your character name EXACTLY how it is in game, and select the server.

By this point it should give you a page to read for the next steps..

On this page it will ask you to login to your lodestone page, with your character from the guild being the active character.. and it will provide you with a generated number.

Place this number in your characters profile information on the lodestone, save, and press proceed on the page from guildwork.

It should tell you if it worked or not, if you followed these steps.. it should work perfectly..
and just a little side note… you can not have anything else in your character profile, ONLY the number it gives you.

Congrats! You've registered your character!