Heavy tanks are a completely different function than regular tanks. They are like a howitzer and tank all in one, minus the shooting over walls. They usually work best with all or mostly heavy tank attacks, rather than mixed in with other troop types. The biggest upside is that if you use them carefully, you can raid continuously without losing anything.
It is certainly worth upgrading the factory, you will want it very much in atomic no matter what (APCs and THs). But it is less a question of incorporating them in your mix, then whether you want to do or try that type of raiding. Make sure you have decent airplanes and the splash damage research in the library before trying them, they will be a lot less effective without splash damage and air support.