Muhammad,
First off, I strongly recommend that inputs be placed on the LEFT of any structures in LabVIEW. Dataflow is typically from left to right.
Second, the determination of whether a tunnel (the "box" you speak of is called a data tunnel) is an output or an input is determined by what it is wired to. Data that originates outside of the structure and is connected to the input of a node inside of the structure (or just connected to the structure) is an input tunnel. Data that originates inside of the structure (the result of an output from a node) is always an output tunnel on that structure. While this is in fact independent of the location on the structure, it is common practice, and recommended, that inputs occur on the left of a structure, and
outputs on the right.
Of course, this all begs the question as to what exactly you are doing that you have a tunnel that is not the input/output that you want.
If this doesn't help, either post again, email me.
Also, pick up a copy of "LabVIEW for Everyone" by Jeffrey Travis, and possibly the LabVIEW Basics I and II CDs from NI. These are the best tools for learning LabVIEW. That, and going through the examples database in LabVIEW.