At this stage, you cannot place a window over another window (in the same wall). You will need to draw the stacked window to the side, and then move it into your desired position (above another window). It is actually quite a quick process.
You can turn off window lintels by clicking on the window options tool, selecting the window that you want to edit, and then turning lintels to off (found in the edit window/door dialogue). Note: This dialogue can sometimes hide behind the main Window Tool dialogue - so simply drag that dialogue out of the way.
We hope this helps.