Currently, there's no such option available in TemplateToaster, when you add content or any module in a module position, the height of the module position will get increase automatically, as it depends upon the content.
But if you want to set the height manually, you can set it by using the custom css, at TemplateToaster- > General -> css
by giving the min-height to Module Positions.
The alignment, for now you can set it by using the padding and margin.
Rest, this suggestion will be forwarded to development team, if it seems feasible, we will try to include it in the next release.