FontCreator uses a script to align diacritics in a nominally correct position. It may work for the Regular typeface without much further adjustment, but for an italic typeface or a handwritten script the user will always have to adjust the position manually. A knowledge of correct positioning is essential.
I developed and maintain the Complete Composites code for FontCreator. It is a plain text XML file that users can edit for themselves to add definitions, or modify the existing ones. I frequently make minor tweaks to the code. This is the definition for U Ogonek:-
<Composite><!-- U Ogonek -->
As you can see, it's fairly easy to understand. I use decimal code-points as I find them easier to understand at a glance than hex codes (which may also be used).