I need to plug in a CF card to an ATMega128 design. Does anyone know the
>best way to go about this, or at least the best place to start looking?
There are many open projects available in the internet that connect CF's to microcontrollers. A good source is i.e. one of the application notes from SanDisk which showes several ways to do this.
In short, it boils down to connecting A0-A2 D0-D7 /IOR, /IOW and /CS and following the protocol specs available from
HTH
Markus