Does anyone have a good tutorial on how to add dashboard options to tweak a theme?

Since I'm running a multisite - rather than removing certain features that I (or my users) don't like in a theme, I'd rather add an option on the dashboard that controls the visiblity.

I haven't developed any themes or plugins myself, so I'm not too sure where to begin. I've been able to remove features entirely from a theme, but gating them by something in the options is a bit more complicated.

Thanks!