On the transfer function magnitude graph, you will not want any deviations of more than +/-3db. However, in most circumstances you should be able to figure the enclosure size for response within +/-1db. Most of the enclosures I have designed with the program are all flat as in they do not deviate from the reference plane (0db) until they approach the tuning frequency (or Fs in the case of sealed) or reach the tuning frequency (or Fs). As I stated before this is going to be the most important thing to look at. If the response is not there, it just won't perform. Only once the response is satisfactory do I begin checking the other parameters to make sure they are in line.
Once the frequency response is the best I can get it, I then check excursion levels to make sure it is not exceeding the limits of the sub. Remember that you can usually exceed linear xmax by 10% before audible distortion. If I am using a vented enclosure, I also check the air speed and/or vent mach to make sure noise should not be a problem. I also then check the impedance curves to see if the sub is a real reactive load or not.
Remember that your results are only as good as what you put in. The more accurate your input parameters, the more accurate the results. If you are fortunate enough to have all of the driver parameters, you will want to shut off the "auto calculate unknowns" feature. Most subs I have seen do not include ALL parameters.