Customize Themes with regular updates

I am using WordPress 3.3.1. and the theme ZeeDisplay 1.0.6..

My question is this: If a theme requires changes to be made in order to have it look how I want, and regular updates keep coming out for both wordpress and the theme itself, what is the most effective way to keep up with this?

–Do people really do these changes every time…by hand…

or

–Are people just finding themes that meet their needs?

or

something else?

I’m trying to not over complicate the way I’m doing things, and I’m the first to admit, I have lots to learn.

my site is – elizabethtownfamily.com