Companies are commanded like single units by simply selecting their flag. This alone keeps Kohan from degenerating into a contest of how fast you can click and drag a mouse. While controlling company units rather than individual units pulls the action up to a more tactical level, this is merely a superficial benefit. The real depth of the company-based system is realized through planning the composition of your units. The composition of each company will determine that unit's distinct capabilities, strengths, weaknesses, etc.
Different combinations produce a variety of results.
For example, a company of Scouts with a pair of Windriders in the support slots would be a fast, highly maneuverable company. Replace the Windriders with a Ranger and a Cleric, and you slow the scouts down, but increase their visual range and provide them healing spells. In addition, you will find that certain types of companies are better suited than others in dealing with the various opponents you will encounter. Not all unit types are available, however, without first meeting certain prerequisites. For example, in order to train Rangers you need a wood mill and a library in your city.