It's amazingly simple....You connect the midi cable from the HD out to the amp in.  Then you press both amp channel switches simultaneously and hold them until Ch1 blinks.  Then you chose your Pod channel (FS5 - FS8) that you want to start with.  Once it's on the correct preset, push the channel on the amp that you want it to change to.  That's it....you're done.  You do that for every preset you'd like to use (I had 5 banks that needed to be set and it took about 3 minutes). 

You have to hit the channel switch on the amp, however.  If you try using your footswitch to program, it won't work.  I had the effects loop on while I was programming, but couldn't tell you if that matters or not.