On his Blues on the Bayou album I think he may have changed settings on a couple of songs based on how the guitar sound varies from one track to another. However, I've seen him like 12 or 13 times in concert and I don't recall him changing it. I can't remember for sure but I think he kept it on setting 2 (maybe).
Word is that B.B. likes position 2 and leaves it there. Apparently this is the choke plus a 0.001uf cap. His tone is often described as being out-of-phase but it's probably more to do with choke in the varitone which can cut quite a lot bass by itself. Chucking in the various caps gives you midrange filtering effects.
I think by the mid to late '60's he was just running his stereo 355s into a single Fender amp with a mono chord and setting his pickup selector in the middle position. That would give him the out-of-phase tone, which he would then dial more in our out by playing with the neck and bridge pickup volume controls. I don't think he used the VT at all.