The pen loop can be attached to the keyboard or the body of the tablet or to the kickstand or you could not use a pen loop and simply clip it to groove in the keyboard or you could buy the Cleanstylus accessory http://cleanint.com/cleanstylus-surface-3/
I bought a carrying bag that negates this issue as it has its own own loop (this is with sp3 but it is no different).
I refuse to use the loop as its just flimsy and I have no trust in it, not to mention awkward, and I refuse to use the clip and groove "just in case"
To me this is one area where ms really need a better solution. I don't like pen silos because then you end up with a craooy Samsung stick that is plain awful to use, but I like the idea of a small silo that the pen clip slots into.
I recommend two pen loops. With only one pen loop it flops around and pulls off easily.
You can clip it to the keyboard, and there is a ridge for it to rest in, but then you have to pull the pen off the keyboard when you want to type.
Avoid the "cleaning" doohickeys. I bought one, and not only is it ugly and inconvenient; it ended up snagging in my bag and ripping the holder off the pen. I complained to them and they basically said you're-holding-it-wrong.
I carry it in my shirt pocket. I do have a bag I carry the computer in, there are places in the bag to keep pens. Since I normally keep my readin glasses and a writing utensil in my shirt pocket, the stylus is no extra burden.