New Central Air Install: choosing single-stage vs dual-stage condensers
2 stage equipment is for comfort, not economy. You probably won't make that extra cost back if used 2 months a year and your house leaks AT ALL. (high SEER units are useless in an improperly insulated house) Reliability is doubled in that half the system can be broke and it will still work. Heating in your area is more important I would think, spend that money on an ECM (variable speed) furnace with a modulating gas valve. If they are the same SEER then there is no operating cost difference (right guys?). A 3 ton will just run less often and cost more to do so than a 2 ton. If you want to save money, thermal scan your house and fix those issues. Unless your rich and a green freak, I see no benefit to dual stage systems less than ~10 tons. The second stage is for those months that your first stage can't handle. In your situation it sounds like it would either always run both or never need the second.

ECM's pay for themselves in about 3 years, MGV's 10 or so depending on usage. 18 SEER will never pay for it self unless your house has an astronomical R value.

Quote from HVAC TALK


  2 Stage is for COMFORT.
  
  Some people may save some money, from the longer run in first stage because they won't feel that sudden coolness from the short on time that a single stage has at the mild and mid range winter temps.
  Meaning they don't set the stat as high as they did with their old unit.(comparing 2 stage 90&#37; to single stage 90%) So it looks like the low fire is saving them a lot of money by being more efficient, when its really because they have their stat set lower.
  
  Same with 2 stage A/C. They may set their stat 1 or 2 degrees higher. So they save because they are more comfortable at a higher temp. Which of course, maintaining a higher temp, uses less electric.
  
  Most 2 stage units going in are replacing older lower efficiency single stage units. Moving up from a 80% to a 90%, or 9 SEER to a 15 SEER, so they see the overall savings. And rave about 2 stage savings.
  Contractors then repeat how much a 2 stage system saved that person.
  
  So its just repeating observations made, without a control, to check it to.
  
  In your case, (not to take money from a contractor, but), I'd just set the lock out lower, and see how it does this winter.
  
  Keep the money you were going to spend on a new system in the bank, and let it make some interest. 


http://hvac-talk.com/vbb/showthread.php?178756-2-stage-furnace-not-more-efficient-than-1-stage/page2

This guy "Beenthere" seams to really know his stuff.