taking vitamins with food is not an issue. Since they occur in food and that is what we are geared for.

But for B12 absorption, assuming failures of normal systems, B12 should be on an empty stomach.

I take mine at night before bed, because I don't eat after dinner.

But you can choose a time convenient for you. Microgram doses of anything in the drug/nutrient world, are best absorbed on an empty stomach. Fiber and other buffers absorb these tiny doses and remove them from the GI lining.
Thyroid meds, and digoxin are examples of drugs that have been found to be not absorbed when food is present. B12 is also a microgram dose...so it follows that empty stomach is best.