Simply change the size on the character after you have applied your appearance : )
EDIT: I assumed you knew where it was: select your character, tab "Control & Physics 1", bottom left of the tab "Scale".
A neat trick is to have a temporary appearance you save at the proper size (the same as in your target scene) and load it. So that you don't have to rescale it afterwards since it might break initial alignments.
Another thing: alignment can be broken simply because of the overall proportions of your other character. Size is not the only factor.