I think an answer may be easy after studying the system from the following points of view ; integrity of the whole system, nature and interactions of the agents related to the system, the interoperability among the subsystems putting in consideration different scale in time and space......successful previous work in this area
In my opinion, Repast Simphony 2.1 (www.http://repast.sourceforge.net/) is the best platform for modeling ABM subsystems. As an example, I suggest the article "Colonist household decisionmaking and land-use change in the Amazon Rainforest: an agent-based simulation" (DOI:10.1068/b3098 - http://www.indiana.edu/~act/files/publications/2004/04-08_ColonistHouseholdDecisionmaking.pdf)
You might want to take a look at Presage2 (http://www.presage2.info). It allows to do more complex things than the usuals ABS platforms such as Repast or NetLogo. While the learning curve might be a bit steeper, it's much more powerful.