In order to include pre-draft trades in your league, you'll need to use the Fully Customized option on the Teams and Draft Order pop up box (Gear Button -> click Teams and Draft Order). Please note that pre-draft trades are those that have been concluded prior to the stat of the live draft - whether one day, one week, or one year in advance. See the graphic below:
To account for trades during a live draft, you'll need to use another interface in the program (under the Gear Button - Trade Players and/or Picks).
In this article I'll cover an example Pre-Draft trade between Team Five and Team Six, in which Team Six got Team Five's first round draft pick while Team Five got Team Six's second and third round picks. First, go to the box in the upper left of the Teams and Draft Order pop-up box and select Fully Customized. Then answer Yes when the Dominator asks if you really want to do this. Then swap pick #5 to Team Six (who now has #5 and #6), scroll down to swap pick #19 to Team 5 (who now has #19 and #20) and pick #30 to Team 5 (who now has #29 and #30 overall).
Once you've made the necessary changes to the Fully Customized draft order to account for all pre-draft trades that impact this year's draft in your league, click the green Done button.