I am in the process of finalizing a few systems designs and have a few questions.  I used Elite RHVAC to perform my manual J loads, and am using WaterFurnace software to size the system to properly handle the heating and cooling loads. 

When I size the system, do I need to worry about getting enough CFM's for the rooms, or is there a way to increase the output from the system?  The design we like to do is one unit for the first floor and then a split system for the second floor with air handler in the attic.  Using the BIN charts, it looks like a 4 ton system would give me efficient load to handle the loads, however, with standard CFM of the equipment, it does not seem large enough. 

Is it possible to satisfy the load and the CFM requirment without using a larger size system?

A little confused by your question so I apologize if Im giving you info you already know

Most systems ask for around 400cfm per ton , little less in heating . Most ecm fans can handle a wide range of parameters

For required cfm per room with enough heat , you first size the floor room by room ( equip size )

then you go room by room get the load per room ( required buth )

the formula for btuh  is  multiply you temp split ( about 30 ) by 1.08 and then by your cfm

so if you know your load call that L   it would look like ------L=30times1.08 times Y  ( now your cfm   )
multiply 30 and 1.08 and divide that from L this should give you your cfm for that room if Im not mistaken
Once you know your required cfm to deleiver the heat required selecting duct size ,location , and returns should all be standard
Just remember to confirm you static pressure to each room after as Im sure you know

This is well outside my scope of work , and is strictly from memory so please feel free to correct me

I use RHVAC as well. If you use the heat or cooling load (whichever requires the most air flow based on the RHVAC output) You can then find a percentage of total load for each room and size your supply and return ducts based on the 400 cfm per ton rule. Because the total load is so small you might consider useing a zoning system to serve the entire house with only one unit. This can save initial cost and preclude the need for the attic unit and the associated service , maintenance and potential water leak problems.

I too use Elite. Individual room loads are provided. While I'm a great fan of zoning, it is limited by the fact that most two stage equipment runs at 70% of full load in low stage. That limits how small individual zones can be. My builder partner likes to install single units in high end three story homes, so I'm ramping up my understanding of the shortcomings and workarounds.

As ever tighter construction materials and techniques result in lower room CFMs, duct register sizing and location become more critical. Any student of this will be well served by understanding the basics of ACCA manual T. Throw, stratification, and attacking each room's sources of load while not creating bothersome noise or uncomfortable drafts all figure into the calculations

Thanks for the advice, while this has helped, there is still one area I am a little uncertain about.  When RHVAC gives me the CFM for each room, should I size the system based on CFM requirements as opposed to solely on the heating and cooling loads that are required?  I've been sizing the systems for 400 CFM/ton. 

After sizing the system, I use WaterFurnace's GeoLink software to size the loops.  When I run the evaluation on the system, the efficiency of the system is usually close to 100% which means that the back up would not kick in unless there is extreme temperatures, as opposed to sizing the system to handle 90-95% of load as I was explained in one of the WaterFurnace trainings.  Is there a way to reduce the tonage on the unit while satisfying CFM requirements, or is it all based on CFM?