While knitting happily along, I was asked about picking up stitches and how it's done. In my humble opinion, I think you should pick up stitches in a way that makes sense, which leaves the smallest mark on your project. I also use a needle one size smaller than the one I'm using for my project.
You might not have two colors to choose from in which case I would make sure that I pick up stitches in the same place for every stitch so that my picked up line stays straight.
In the case of the Sipalu Bag where you have to pick up a lot of stitches (a lot!), the way that made the most sense was to pick up the pink bumps (not the red) because I don't want to get the red yarn on the pink:
That way I end up with only pink stitches on both needles:
Then, when I knit the stitches together there's no red showing through.