Can I use a stereo jack for the switched jack? I tried that and it doesn't seem to work. I guess a newb question, but is there a difference from a stereo jack and a switched jack?
No you cannot, if you did you would have to a patch cable plugged in.
A stereo jack is just that, for stereo operation, it has the tip ring and sleeve on it. A switched jack is a mono jack that shunts when there is no jack inserted.
So with the duo phase if you wanted to just run into the first input and out of the second output, you would be able to without a patch cable running between the two pedals.