How to set Multi Layer Check in Altium 14?
I haven't gotten really familiar with AD 14 yet, but you could just write two rules, Top_Clearance and Bottom_Clearance.

Top clearance has
Where The First Object Matches: Layer Top

Where The Second Object Matches: Layer Top

Bottom_Clearance is similar. Although I've never seen a clearance check problem between two LAYERS. If I remember correctly, this is how AD 10 works too. Maybe you need to define some more accurate/realistic 3D bodies? Or maybe I don't fully understand your problem.