I just checked the Roll20 sheet, and if you click the settings gear icon on the sheet you have the option to add Deep Cuts modules at the top.

Per default that is true, indeed I forgot to mention that I'm talking about a special case.
When you get bonus die through help or abilities you would just roll 1 dice instead of 2 keep the lowest. But when you get bonus die because of additional threats, you would have to roll 2 keep the lowest to generate one outcome and rate the bonus die seperately to allocate to the threats.