Ryan,
I have a decent amount of experience (i.e. it is my voice on the videos, I helped with the concept and I am really good friends with the guy that created it). Some things you should understand. The alignment feature is really designed for a two printer setup like the
DTG Digital Eclipse. It will allow you to adjust the print from one printer to a 2nd printer in the same line. I don't think it will provide you the answer to what you are looking for.
As for the Channel Flush feature, this feature will "print" ink out of specific channels that you desire. This feature does not use the suction / vacuum pump to suck out the clogs from the print head. Thus, I recommend the Channel Flush only when you have a clog of less than 50% of the nozzles. Otherwise, you are going to need to use the vacuum pump.
However, there are two other features that might help prevent the clogs from occuring. Check out the videos on the Time Test Print (prints out a small test pattern that fires ink from just the channels you desire based on the schedule you set) and the Timed Clean (runs a head clean based on the schedule you set). You can check out all the videos on this link -
YouTube - Broadcast Yourself..
Hope this answers some of your questions. If not, feel free to ask them.
Mark