80% vs 90% Gas Furnace
Installing a new gas furnace is not a simple or cheap endeavor. They say Knowledge is power but it can also ensure you are getting the right furnace for the correct application. When it comes to a gas furnace you have several options to choose from. Depending on your specific set of circumstances one type of gas furnace may benefit you more than the others. You have two basic types of Gas Furnaces: 80% and 90%

The differences were explained to me a long time ago in a way I found very simple to understand. For every hard earned dollar you spend heating your home with a 80% efficient gas furnace basically 20 cents goes up and out the flue pipe while the other 80 cents is used to actually heat your home. A 96% efficient gas furnace allows you to utilize 96 cents of every dollar to heat your home where only 6 cents is waisted up and out the flue pipe.

Why would I ever install anything but a 96% gas furnace in my home???
The one thing you have to know about a 96% efficient gas furnace is that it produces water in the process of making it so efficient. In the winter time when the gas furnace runs the water being drained from the unit can possibly freeze up depending on where the furnace is located (example in your attic) or where the water is being discharged to example outside of your home again where it may be well below freezing. The other major factor is the cost difference between an 80% gas furnace and one that is 96% efficient. The more efficient the more the cost of the product. There are more parts and technology involved in the higher efficiency furnaces than in the 80% version. Thus the cost difference between the two can be quite different.

My Suggestions
If you live in a two story home I would suggest the main floor of the home be served by a higher efficient gas furnace while the upstairs unit could be an 80% gas furnace. The reasoning behind this is based off of the principle of hot air rises. The air from downstairs will travel up stairs assisting the heat requirements. This typically means the downstairs unit will run more and consume more fuel where as the upstairs will not run as much. If you have a single story home with just one unit I would strongly suggest paying the difference and upgrading to the 96% gas furnace as you will reap the benefits of consuming less fuel monthly.