Yes, MVP and HOF users can customize the order of any draft. To adjust a draft order, simply navigate to your My Account page. Then select the appropriate league from the ‘My Leagues’ list and click the ‘Draft Details’ option. You’ll be able to alter the order of your draft board to re-assign any picks that have been traded.
If the league was imported via sync, then you can duplicate the league, and then click the ‘Draft Details’ option on the duplicated league to account for the traded picks. This will work for using the Draft Simulator and the Manual Draft Assistant. If you're using the Sync Assistant, then you must use the league you imported via sync when it's time to use the Sync Assistant, and the tool will pick up the traded pick data from your league's draft room upon launching the Sync Assistant.