If we are studying a single or two body system, then there is no issue. However, let us consider an illustration here as shown in the figure. There are possibilities of having different combination of bodies constituting different body systems.

Identifying body system |
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in selection of a body system, the guiding principle is to treat bodies as a single body system, when we know that bodies have common acceleration.

In the figure, the objects numbered 2 and 3 can be considered a single body system as two bodies have same acceleration. The objects 3 and 4 can not be combined as a single body system as they have acceleration of same magnitude, but with different direction. The objects 1 and 2 can be treated as a single body system, if two bodies do not have relative motion with respect to each other. Otherwise, we would need to treat them as separate body systems.

It is not always required that we must know the direction of acceleration before hand. We can assume a direction with respect to one body system and then proceed to find the directions of the accelerations of the other body systems in the arrangement. Even if our assumption about the direction of acceleration is incorrect, the solution of the problem automatically corrects the direction. We shall see this aspect while working with specially designed example, higlighting the issue.

But the basic question is to know : why should be look for more than one body system in the first place? It is because such considerations will yield different sets of equations involving laws of motion and thus facilitate solution of the problem in hand.