When you are writing content with two voices sharing the same staff, Flat put the stems of one voice upward, and the stems of the other voice are facing downward.
Sometime the stems direction is not the more appropriate:
We just added a tool that comes handy in this kind of situations: you can now swap the voices assigned to the selection. To do so, make a range selection, then click on the voices button. Finally, click on the Swap voice button.
I hope this tool will make the composition process easier for you!