There are basic setup instructions here:
PT3 Documentation. However, there are some things that aren't documented you will want to know. First off, clicking on the PT3 icon on the table will pull down menu selections for setting stats on the HUDs you see. Secondly, if you right click and drag, you can move HUDs around the table. Once where you want, click the PT3 icon and click "save layout" to save where it is. This goes for muck card HUDs as well. Hope this gives you a good start at HUDs and how to change them.
~ Thomas
[Pokertracker support]