I think I understand what the first part is saying.
The stitches on the holder for your thumb kind of represent a hole in the fabric. If you think of that hole as a slit, there are some corresponding stitches above it. (You probably cast them on after you put the thumb stitches on a holder.)
So you'd pick up and knit those stitches. Amy has a video of picking up stitches, if that is giving you trouble. It's on this page: http://www.knittinghelp.com/knitting...iques/misc.php
. Scroll down to find the video.
I'm not quite sure about the other part of your question -- I'm having trouble visualizing it. Maybe once you have the stitches on the needles it will be more obvious to you. If you picked up stitches other than the three in your first question, that might be where the decreases are -- it might just be a way to eliminate possible holes by having you pick up more stitches than necessary, then decrease them out so you have the right number for the thumb.
Hope some of that at least helps.