When considering the guidelines to follow for the orientation of chemical structures, perhaps the most important thing to keep in mind is that, as far as chemical meaning is concerned, they do not matter. Simple rotation of a chemical structure within the plane of the diagram will never affect its chemical meaning. Flipping a portion of a structure requires a corresponding adjustment of stereochemistry indicators, but changes nothing otherwise. In terms of chemical meaning, the orientation of structures is irrelevent.
On the other hand, practicing chemists generally have an idea of the orientations they expect. This is especially true for various classes of biological molecules, and particularly for those with multiple asymmetric centers, but it is an issue for all structures to some extent. Although benzene could be drawn in any orientation (as shown at right, above), most chemists would expect to see it with "points up and down" or possibly with "points left and right" (left and center structures above, respectively). So, selecting a reasonable orientation for chemical structures serves only to present chemical information in a way that is most convenient and least surprising to other chemists. That is still important, for sure, but nowhere near as important as making sure that the chemical structure itself is as accurate as possible, whatever its orientation.
Selection of a reasonable orientation is an art form even more so than other aspects of structure representation. It is therefore worth emphasizing again, that these guidelines are only guidelines. They are provided so that an author who wants to "follow the rules" has some rules to follow. They are not expected to be comprehensive for all possible chemical structures, and they are certainly not indended to be definitive. If you have a structure that you think looks better if these guidelines are not followed, then by all means draw it in the way that looks best to you. There is absolutely no problem with that.
