Armature at Wrong Angles

A little trouble with modifying an already existing armature - help greatly appreciated.

I imported an armature from Studio Max 3DS for a project and the orientation of the bones seems to be off. All of them seem to be more or less horizontal, even though they are supposed to be vertically attached to one another. The problem is not the animation/bone connectivity because the walk animation works just fine; the bones just look splayed out in different directions. I tried to reorient the bones manually by making them parents of each other - so that it would look more human. But this changes the animation, and I don’t want that! Any way to fix this?

(small picture of issue)

Looks to me when rig was imported the rigging retained parent child relationship correctly. But bone axis seems differently represented on 3DS Max. So, you lost head to tail connection in Blender.

I suppose the best and easy way to deal with this problem is to use Custom Shape for bones that you need to use. And, move other bones in to different layer.

Does that mean I’m essentially creating a new armature? How do I rig the bones so that the new ones will be in the original bones’ positions and relationships? Thanks.