Adding to this, just get your fingers used to the hotkeys for courier stuff. I have F2 as my courier select, then the standard QWERDF for it's abilities. I when I want to send it to secret shop, I just know from muscle memory to hit F2, W, R (for speed burst), F1 (select my hero again) and I don't have to look at my hero. Also if you have quickbuy on, you can just select the courier when it's at the Secret Shop and hit the quickbuy key, then just send it back to base or send it to you, or whatever you're doing with it from there. If it's going across hostile territory, then shift queue some moves in there using the minimap. If you have it go along the edge, the other team won't be able to touch it.
People were (probably jokingly) commenting on my bottle crowing when I was at mid earlier if I couldn't get to the runes first. I was just hitting F2, right clicking myself, F1, and as soon as the courier got to me, drag the bottle onto it, then hit F2, Q, hold shift and hit Q, D (if there was other stuff to grab out of stash), and F. I learned this the hard way in the past, but just hitting D then F WILL NOT refill your bottle. It actually has to go into the fountain to refill it, whereas to grab items it just has to touch the edge of the fountain.
Also always give the thing a haste! If you see that little boot in the lower right corner of the screen, that's your queue to hit F2, R, F1. You can do all of this stuff without even looking at the courier.
It's like the one time I actually want to queue commands up for the courier. Most of the time I'll just wait until I know I'm in a safe area and hit the button in the bottom right. You know, where the minimap should be. 
