The bone structure is probably displaced because the character's yTrans value isn't zero. For some reason, a lot of figures are like that by default. I prepare the donor figure beforehand. That means disabling IK, zeroing all the joints (with the Joint Editor), making sure all the trans values for Body and hip are set to zero, and memorizing these settings (Edit menu --> Memorize --> Figure). Once this is done, save it to the Library and then load that in the Setup Room for your bone structure. You might also want to strip all the morphs from the donor figure, by hand or with Morph Manager, since they probably won't be compatible with the clothing mesh you're poserizing, and you'd have to remove them afterward anyway.