I have laminate flooring but several floor mats (small rugs) here and there. I've had to clean them occasionally when there was an accident during their potty training. In the beginning I had to take away all the mats.
Luckily Casie who uses indoor potty pads eventually learned that my mats are no-no's, so I'm able to put a few back out. Now, instead I see her running over to the pee pads. Yay!
I still always tell her "good girl!!" when I see she peed on the pad. I'd definitely would isolate them from the carpeted areas during potty (and re-potty) training!