How to join contours depends on which version of FontCreator you’re using. With the 30-day free trial, which is the same as the full professional edition, it is easy. You just select two or more overlapping contours in contour mode, and use “Get Union of Contours” from the toolbar.
With the Home Edition, you have to select two nodes — one on each contour — in points mode, right-click, and select join contours.
See this tutorial on making Æ and æ ligatures for illustrations of each method.