Yes, MVP and HOF users can customize the order of any draft to account for traded picks. To account for traded picks, navigate to your My Account page. Then select the appropriate league from the "My Leagues" list. Delete any Draft Assistants you have open and click on "Edit" under 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 you're using the Draft Assistant w/ Sync for your real draft and haven't had time to customize your Draft Details, then don't worry. Once your real draft starts and you launch the Draft Assistant w/ Sync, the Assistant will automatically detect and pull in any traded picks.