Most leagues will either have a SERPENTINE or NON-SERPENTINE style draft order, which FanDraft fully supports.
FanDraft also supports CUSTOM orders, such as 3rd Round Reversal where the direction changes in individual rounds.
However, if your league has a completely different draft order in different rounds, the only way to set this up is through the PICKS TRADES area. You can access this area only after you have "Finalized Your Draft Order".
In this area, you will be able to set each and every individual pick of your draft.
To perform this, click on the PICK TRADES tab. After you enter this area, you can change each specific pick by changing the teams in the drop-down area.
Click on the ROUND TO EDIT drop-down to change the round you would like to edit.
Note: Because a standard draft board works in a column/row type grid, if you have a different draft order for multiple/all rounds, the "Draft Board Display" will appear rather confusing and so you will likely want to utilize either the "Roster Board" or "Player Board" displays during your draft instead: