I am interested if there is a better way than what I am about to describe, because I too am new to these features and am just starting to get into trading. Haven't completed one yet, and of course the first one I try, something (minor) went wrong so now its delayed. Anyway...
Yes, use "Auto mark unused for trade". I also created a "Do-not-trade" tag for items I know will be put into a deck soon. So you can press the auto-trade button, then immediately filter your trade list by the do not trade tag, and remove those from the list.