Is there a way to specify module dimensions in the backend and not just margin, padding etc?
I.E) I want all the maintop A, B, & C twitter/news feeds to be level at their bottoms for a nice clean look, but obviously each is bringing in different feeds with different # of characters ... that ends up in heights that range by a few pixels and look messy
No, you can't do that from the backend. You could maybe limit those heights through the css by applying max-height value to a module divs in that module position. YOu have to place this css code in custom css file
When we release upgrades template files will change and you will have to reapply all your changes again (that's if you can remember where they all are). If you keep your changes in a separate Custom CSS file you'll have no issues upgrading.