There are several reasons why it may be advisable to use two smaller units than one large one. The use of two or more small units is referred to in the HVAC trade as "zoning." Generally a separate zone is established if one or more of the following criteria apply: the area has a specific use distinct from the rest of the home (mother-in-law's apartment), the area is maintained at a distinct temperature (basement), a separate level of the home (2nd floor bedrooms).
An additional reason for using two systems is that the equipment of many manufacturers falls off in performance above four tons. As a result, the use of two 3-ton units is likely to yield a higher performance than a single 6- or 7-ton unit. This performance difference, however, is not sufficient to justify the additional cost of the 2-system design.