Like you, I never did crate training, and sometimes wonder if I should have. Instead I started pups out in a playpen, then on to the small ex-pen that I LOVE. Even though they mostly have free run, I occasionally put them in the ex-pen for various safety reasons, and they actually enjoy it and go in willingly a lot. The one I got is in this thread:
http://www.yorkietalk.com/forums/yor...ve-ex-pen.html
Also, congratulations on your new tile; good choice for a house with dogs. I love mine, though I understand people in colder climates might not. About grout, when it is thoroughly dry & cured, have it sealed and it will be very cleanable. It won't get ruined by pet spots.
I can't wait to get rid of the upstairs carpet in my house, though I'm not totally settled on hardwood yet.