Those are tool loops. basically they are used to hold the bottom end of an ice axe or trekking pole onto the back of your pack.

Here's an example of how they are used, with the head of an ice axe




Now to answer your question, my sleeping pad is usually either inside my pack, (rolled up in a big tube with everything stuffed inside, or folded up against the back of my pack inside, or, strapped vertically to the outside, when I'm carrying a smaller pack and don't have room in it...

For example (with the smaller pack)





but most of the time I keep it inside the pack. especially if it is an inflatable (in the picture above I'm hammocking so I just have a wide blue closed cell pad..)