Almost always "pick up stitches" means "pick up and knit" as illustrated by Amy on this site. You'll go in from the front, stick your needle towards the back, wrap like you usually do, and pull it back through. You'll then have a stitch on your needle.
When you're done picking up and knitting these 90 stitches, you turn around and start purling a row on them.
The other method you were thinking of -- sticking your needle through all the stitches, then attaching your yarn and knitting them -- can distort your fabric.