I'm trying to build a Mace that has a base 1H 2d6 and 2H 3d6 plus 1d4 sonic damage for thunderclap.  I'm having difficulty in managing the base damage dice.  I can add a modifier, but it doesn't roll the modifier when I click on the radio button to roll the digital dice.  Is there a way to change the base damage dice?  

Not at this time, no.

And the way the Versatile weapon property works, when the weapon goes from One-Handed to Two-Handed, it wouldn’t go from 2d6 to 3d6, it would go from 2d6 to 2d8.

Thanks for the reply and the reminder of the versatile weapon rule. You are absolutely correct.  This particular weapon is a DM Homebrew that breaks the versatile weapon rule.  I'm attempting to take his notes and build it into DND Beyond.   As a workaround I"m inserting information  in the modifier section simply as a reminder when I roll, then will add the appropriate digital dice to the roll and add together with the damage roll.  Not as slick, but works.  Thanks again for the reply, it at least lets me quit trying to find the magic checkbox to make it work. 

Yeah, a lot of us have been eagerly awaiting the ability to alter base weapon damage. Range too. And if it it has to be the 3d6 then you can’t even get away with just adding versatile. The upshot is that DDB is currently trying to figure it out since they have to for stuff like [Tooltip Not Found]. So that extra 1d4 should work at some point. But temporary effects are not yet supported so if you use the damage modifier to add the extra 1d6 then it’s gonna do it all the time. Yeah, I can’t see any other way to do it than what you are planning.

I've played around with it, and it works fairly well.  Just have to add the two totals together. No big deal as a workaround until DDB gets that far in their content.  The whole system is pretty awesome, so no complaints here. With the digital dice, I can at least just go play with my iPad.  Nothing else to carry.  Thanks again for the thought you put into it. Great community here.