I struggled a bit at first, but it gets easier. Here's an example screen:
So, here's a hierarchy of how I lay things out (not sure of this is the proper way, but it works for me):
Project
-- Frame (if screen can co-exist with others) or a dialog (if a screen should take all focus away from its parent)
-----Panel
-------PanelSizer (vertical)
---------Horizontal sizer for each row
Once you've got them all into position, you just need to play with the proportion settings of each component on each sizer. Once this is done, I copy the code, refactor and then tweak manually to line things up.
The code that comes out of wxFormBuilder is relatively clean. I guess that anything that comes out of a "drag and drop" designer tends to be messy as it has to worry about the absolute positioning of each component (this might also cause all kinds of issues when expanding the window).