It seems like everyone has different opinions, most with minor variations. When I first practiced steeping, I assumed leaving the caps off was a bad idea as PG and VG are hygroscopic, and I didn't want my juices to absorb any sort of moisture outside of the bottles. Now that I've been at it a while, I find that they do in fact steep much better with the tops off for some time. I don't always find time (or remember) to shake my bottles, but it doesn't seem to matter too much as they usually turn out fine if I leave them alone for the most part. I'm sure shaking does help to speed the process along a bit, but I don't think it's absolutely necessary.
So tops off in a reasonably dark environment is all you really need, in my experience. Some liquids take less time to steep than others, so give 'em a good whiff once in a while to see if you notice any changes in smell. If you have a dripping atomizer on hand, it's convenient to sample a few drops every once in a while, too.