NOT SO FAST!
Two ways to do this. As said below, you can use the FX Loop. For dirty patches, I would put all your processing in Channel A and put the FX Loop right before the mixer. Connect the FX Send to your amp. Mute both Channels in the Mixer. So you are only sending to the amp via the FX Loop, and on patches where you send to your amp that way, you mute the mixer to prevent any signal going anywhere else via the other outputs.
For acoustic patches, don't use the FX Loop. Set the Mixer levels how you like them. Use the XLR send to send the signal to the board. Nothing is going to your amp - only to the board.
The other way:
For your acoustic patches, put all your processing in Channel A and pan Channel A full left in the Mixer. Mute Channel B. Attach the left XLR to the board.
For your dirty patches, put all your processing in Channel B and pan Channel B full right in the Mixer. Mute channel A. Attach the right 1/4" out to your amp. Attach a dummy 1/4" cable in the right 1/4" output, otherwise the Pod will sum your signal to mono for the 1/4" outs, so your acoustic patches would get sent to your amp as well as the board.