Why would you think using dog toothpaste is bad in some way? -- it's no more "goop" than the toothpaste you use on yourself. (In fact, I'm wondering why there isn't enzymatic toothpaste for humans like there is for dogs, it seems a more active formulation!)
My understanding is that it's food that generates the plaque, so I try to brush my dog's teeth after her last treats of the evening, the same as I'd do for myself if I were only brushing once a day.
I've also begun rubbing some Wysong Denta Treat on my dog's molars after I brush, and it seems to help. One tooth that looked a little grimy in a crevice even with brushing seems to be improving a bit.