Lets say I don't want to work inverted. How would I keep the Atmel's high going to affect the rest of my circuitry? Has anyone found a good practical method?

Hallo Roelf,

i'm not quite clear what you mean? You only need to invert signal again, and all is fine. There are many latches and buffers arround which internally are inverting signal. So, you do not need additional circuitry.

Bye,
Kai