Glass is susceptible to marring, scratching, hazing, and streaking just like paint. Though it doesn't scratch as easily.
You asked "Should I use the same care on my glass and windows as I use on my paint?"
Are you serious? Do you know where you are? LOL....I'm just kidding. That just seemed like an odd question.
Anyway, you probably don't need to use your "good" MF towels if you have some decent ones that are clean. I keep a bin full of those junky, 10 for $8.99, Microfiber towels and they work fine on stuff like windows. I save my good ones for the paint.
You window should be cleaned whenver you wash your car. Nothing pisses me off more than someone who spends a significant amount of time cleaning their car then skimps when it comes to the windows. It's a chore, and its easy to overlook, but to me it makes a huge difference.
I also use Stoners Invisible Glass. I also use Rain-X. People say it streaks but if you use a PowerBall to buff it off you will get great results. Also, I've heard of people waxing their windshields, but in my experience wax does not buff easily off of glass. Mothers also promotes thier chrome cleaner as an excellent glass cleaner. I dont know if other brands do the same.
If you are going to clay the car, make sure you clay the windows too.