It's depends on how you wanted to do the overmold (entirely upto the part complexcity)
You can do the first shot in one mold and do the second shot in another mold (In two different machines) or first shot and second shot in the same mold/same machine rotated 180 degrees (with a two shot molding machine)
These are completely upto the part shape/size and material.
We usually design these in- or at least add notes to drawings stating where they should not be. Especially if its important that the paths/runners between parts occur in certain locations only.
Thank you John & Pasi
I think I'll go with Pasi's suggestion since we don't care where the paths/runner are (long as they are underneath) and the mold maker is unclear at this point.