Consider two blocks stacked on top of one another. There is friction between the blocks but there is no friction between the lower block and the table. So the only frictional force that tends to retard the lower block is due to the friction between the blocks right? And the force that accelerates the body on top is only the frictional force? Also, I fail to understand how there are different conditions for relative motion to occur between the blocks when the force is applied on the lower/upper block.
In this totally hypothetical situation, everything you said is correct. It's important to remember, however, that there must be a normal force between the bodies for the friction force to exist. In the most intuitive example, this force can be the reaction of the gravitational force (from Earth) from the upper body onto the lower one.
The only acceleration acting on the upper body is due to friction and the reaction to it is the only retarding force on the lower body.
As for the relative motion, in my understanding there are no different conditions depending on whether block the force is applied on. Of course, the block on which the force is being applied would move a larger distance (at a same time interval) than the other.
I apologize for my terrible English.