sikorajm, since you are referring to my article, I thought I better respond. First, just to clarify one thing, I didn't exactly say the blues & pentatonic scale is used over the majority of R&B music. That may well be, but what I said is those scales are used extensively in blues and R&B. A slight difference in meaning; the blues/pentatonic scales are rarely used exclusively. They are mixed in with other sounds.
To answer your question, it of course comes down to using your ear. But to be specific, let's take a 12 bar blues for example.
You can play a minor pentatonic or a minor blues scale (minor pentatonic with b5), based on the tonic, through the entire progression. If you choose to use a major pentatonic, you have to change it when the chords change. So on the I7 chord you can use a I maj pentatonic, on the IV chord a IV maj pentatonic, and on the V chord a V maj pentatonic.
Example in C blues: Use the C (minor) blues scale throughout. Or use a C maj pentatonic over C7, F maj pentatonic over F7, G maj pentatonic over G7.
OR, you can use the I maj pentatonic on the I chord, then switch to a minor blues scale, based on the tonic, on the IV chord. Etc. So, in that C blues: C maj pentatonic over C7, C blues scale over F7. And so on.
But you really, really, really, can't just follow 'rules' like this by rote and sound good. It won't work that way. You have to use your ear, listen to how it's done on recordings, experiment, listen some more to the recordings, learn the actual chord tones, learn to play phrases, and get the rhythm/groove happening, etc.
Did I mention to listen to recordings?