I agree with Mike. It is typically best to set each of the emitters to a specific port...especially if you have two like devices in the system, such as two satellite boxes. This will only alter how the remote sends a signal to the device and should not cause problems with the functionality of your devices.
Yes, a punch through can only be done through the corresponding hard buttons. If you want to use LCD buttons, you can create shortcuts. This is done within the Edit & Label Buttons window...select the button you want, then the device you want to take the command from, select the IR command from that device, and lastly name the button and save it.
Let me know if this helps.
Thank you,
Damon DG
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