Hi Bob,
For each Flex component, there are two component types to choose from, depending on the modeling situation. There are 'Standard' components and 'Single-Face-Cutting' components (Not wall cutting!).
Standard: The standard components are the kind you can place anywhere, rotate them, scale them, move them - they don't stick to any faces, and they don't have any wall geometry included in them. They are suitable for if you have pre-cut holes. (So for the example you showed, where there is a pre-cut hole on the left, you'd want to use a 'Standard' component).
Cutting: The cutting components stick to the faces you place them on, and by default they cut through a single face, as long as they are placed directly on the geometry they are cutting. They can be used in two different situations:
For mass modeling with walls that have no thickness (single face). The cutting components cut through the face, and come with their own wall geometry. (You can change the wall thickness from within the component settings). This is very convenient for quick modeling of exteriors, where the interior is not important.
In combination with 3rd party plugins, like 'double-cut', you can cut through double-faced walls (which I believe is what you were trying to do with the window on the right).
Flex components and the double-cut plugin work together, but I don't feel it is a complete solution. There are still some issues that need ironing out.
To toggle between 'standard' and 'cutting' components:
When button is de-pressed - Clicking on a component will pull in the 'standard' version of it.
When button is pressed - Clicking on a component will pull in the 'single-face cutting' version of it.