Late response here but I just went through the setup process with Enchant 1300 + Harmony and ran into the same issue. My solution is to assign "presets" with the original Enchant remote. It will store volume level, sound mode, and input selection to each of 5 individual presets.

The harmony can call up individual presets, though I found switching between two of them requires two taps of the preset. In my Harmony setup for a given action, I have it power up everything, then do Enchant Preset 1, pause 1 sec, Enchant Preset 1 again and so far it's working well.