When scientists say they are more similar, to they refer to bone structure or genetic similarities?
Both. In simple terms placentals and marsupials differ in their morphology, the epipubis is apparantly a dead giveaway.
Genetically, a marsupial mouse is closer to a kangaroo than it is to a placental mouse. An interesting thread that covered this issue can be found
here - I give you the last post, because it is only the last half of this thread that goes into it, so work backwards. A better, but shorter thread might be
Sequence comparisons (Bioinformatics?).
but exactly which lines is more obvious to scientists?
With both the genetic and morphological data in front of them, I'd imagine the genetic data would be much more obvious. However, the genetic data is a little harder to get hold of
Hopefully that should start you in the right direction.