Does it look better get As in regular prereq courses or Bs in Honors prereq courses?

It looks better to get A's in basket weaving vs. a B in Honors Advanced "You member of Mensa" Ancient Arabic.

I know, it makes no sense, but it doesn't matter. Get A's in regular courses. No one cares what "quality" they are. You get no additional notes on your application. On your app - you will literally enter the grade. Then they calculate your gpas for science, overall, etc. No one cares how special or not special the class was. All that matters is you took it.

Get them done, and be smart about it. Take the teachers that are known to be human instead of the ones that "teach you a lot, but you have a 90% chance of making a C."

You get no points for learning extra, being tough, or taking the path with the most resistance in it. If you want to learn extra physics for the MCAT or life - read some extra books during your MCAT prep or on a free Saturday night. For medical school prereqs, take the course where you are likely to get an A.

Good luck!