I put my pen loop on the back of the SP3 just above the kickstand on the left side (putting the top of the loop just below the volume rocker. The loop sticks out some so that the pen isn't against the body of the SP3 unless it's pushed against the body by an outside object etc. It's out of the way there and really doesn't smack things very much when moving the SP3. I considered putting it on the type cover, but I could see that would cause the pen to flop around a lot while raising/lowering the type cover allowing the pen to possibly strike whatever the SP3 would be setting on.
I doubt any location is perfect, but not a bad location considering. I also thought about putting it in my sleeve for the SP3, but my sleeve is only used when I take the SP3 out of the house. That means the pen would usually be somewhere I wasn't if I decided to use it...then after taking it from the sleeve I'd have to remember to put it back in the sleeve. I like having it attached to my SP3; easier for me to keep track of it and it's always handy if I need it. Like someone said...1st world problems.