You can do it a couple of ways:
You can go into the drawing library and adjust the relevant height ... which to be fair, is a little cumbersome. However, this is the only way I know of to add multiple sections to the transom if they are required, and It's quite a powerful means of making custom assemblies.
OR depending on whether you want to adjust the window or the transom ...
If it's the window ... You can add the same window, uncheck product, edit the window to make it deeper and then ADD PRODUCT CODE, then add a transom.
If it's the transom ... I'd do basically the same, uncheck product, ADD PRODUCT CODE and make it XXXXX - 2, so you have 2 versions of the same window. Then when you add the transom, it will ask you for a size again. That should keep the schedule correct.
Unchecking PRODUCT CODE, editing the window and ADD PRODUCT CODE is by far the quickest way to build up a comprehensive window library.