Does anyone know how to make this work effectively? Everytime you try to move a brush after you have rotated it, it turns into something like totally different. Any help would be appreciated.

Brushes want to snap to the grid by default. You can turn this off however you can end up with leaks etc. If you want brushes rotated, best thing to do is use a set of patch meshes and rotate those. That way you'll know to not even attempt to use them for the hull and they don't snap to the grid.

Patch meshes? I'm not exactly sure what you mean. But the entire brush twists and mangles itself . . . are we talking about the same thing?

Yes, brushes work to the grid (unless you turn it off - which is not a good idea for brush work).

Patch meshes are those things you can drag into any shape you like but start of as a 2d flat plane. One you make one, you can hit V to drag parts of them around to create smooth surfaces.

Patch meshes cannot be part of the hull of your map as they don't block vis. On the bright side if used inside your map they don't have to be aligned to the grid which means free rotation of them is fine and they will not deform.