Gill 2-stage is the best option for Houston but may not be the answer you are looking for. The most important thing is go with a variable speed furnace.
If you have a home built in 1999 in Houston and you have 8-tons on 3200 sq.ft. unless you have a great deal of western glass you are oversized.
The main thing you need in Houston is a tight duct system, sufficient return air capacity and proper attic insulation and ventilation, there are many companies that are getting into attic insulation now and they go overboard and create more problems than they cure.
First start with a properly performed load calculation not one performed to prove out the contractors equipment choice.
Depending on the layout of your home you may be an excellent choice for a single zoned system instead of two systems.
Remember the value of a system is in the install and the thought that goes into the design of that system not hyperbole or low price.