Add the Windowgrouper applet to a panel like you would any other applet, by right clicking on the panel and selecting Add to Panel... Select the Windowgrouper applet from the Desktop & Windows section.
Clicking on the running applet will change the mouse pointer to the crosshairs cursor and a status window will appear in the middle of the screen to indicate that you can select a window. If you now click on a window a menu will pop up that allows you to assign the window to a group.
If you right click on the applet and select Collect New Group from the menu, you can click on a series of windows to add them all to a new group. When you're done selecting windows, just click on the desktop, the panel, or the Windowgrouper status window. You can cancel with the Escape key.
When one window in a group is hidden or minimized, so are the other members of the group. The same is true when a window is unminimized. Additionally, moving a window to a different workspace will move the other group members as well.