A two color model is actually two models that print on top of each other. One is done with one extruder while the other is done with the other extruder. So typically you would arrange the model so each layer gets passes from each extruder.
As for special format, there is none. You just need the two models representing each color, a slicer capable of combining them and creating one file and a dual extruder printer.
Furthermore if you have quality hotend such as an E3D then even after setting for an hour or so a clog should not be an issue. Typically clogs are caused by sitting and not printing come from the fact you are already printing at too high of a temperature. You want the very minimum temp that will work for all phases of the print. Short passes, long passes, dense infill, or sparse infill and so on. Typically you want the min temp that will work with dense infill and long passes and the rest should fall in place.
Everything in 3D printing is a balance. You want the minimum temp possible to achieve the results you want. You want the most speed at the minimum sacrifice of quality. For most people they want quality, speed, and ease of use. Sadly you can never have all three at once. That's just the way it is. 3D printing regardless of marketing hype is not a consumer market yet. It is still a hobby market. Just look at all the "help me" threads for the so called plug and play XYZ machines.
The image below was a dual color print I made long ago. In it you will see the two individual models used to create the single model in the middle.
