Many fantasy players like to run multiple best ball leagues. The Draft Dominator has storage for both leagues and drafts. Each league may have multiple drafts. Please note that team names and draft orders are stored at the league level and not the draft level.
Therefore please ensure when adding a second best ball draft, you use the "Add New League" button on the add draft screen to add a separate league with a separate set of teams and draft order.
Unfortunately there is not currently a way to duplicate the other settings from one league to another.
The second thing to ensure is that you have turned on the best ball/draftmaster setting.
This can be found under Draft Settings > Basic Settings. If the circle is to the right of the toggle, it's turned on.
This will have the effect of modifying positional need balances to optimize for best ball drafts, as well as raising players up the rankings who tend to be more unpredictable, week to week. A good example based on past performances might be Amari Cooper; in standard redraft it's impossible to know when he's going to put up a huge game and fantasy rosters have to suffer many low scores to gain his big weeks. In best ball however he'll be automatically benched those weeks he doesn't perform.