I am looking at building 2450sf 2 story house with approximately 1200sf basement.  Will infloor heating in the basement be cost effective and help on energy efficiancy for the entire house?  Also, do I need a seperate system to add infloor heating to the garage? 

If you put tube in the basement slab you are Radiant Floor Ready® and can choose to heat the space or not. Radiant floor heating does lower the heat load of any building and more important, will increase comfort and may increase the operating efficiency of the heating system if matched with the properly sized ModCon high efficiency condensing boiler.

For the perfect high efficiency water heater (no not a tankless water heater), a companion or "indirect-fired" water heater coupled with a 95% AFUE boiler is incomparable.

The garage may be added with a separate manifold and thermostat.

Get professional design help before you start.

A large, low temperature radiator (like infloor) also helps with geothermal heating efficiency. The trick is to quantify the savings. Probably not enough to pay for itself unless you also value the increased comfort.