The straightforward way to do this is to find the settings dialog in PCMANFM (aka, "The File Manager in Raspbian") and figure out how to disable automounting.
After you do this, then things will no longer automount (you may have to reboot for this to take effect - I am not sure). Now, you can do all your own mounting and unmounting. Fun, fun, fun!
Another way, that I've been playing with lately, is to use mount's --bind option, to create an "alias" of the original mount (the one in /media/pi). I do this:
$ mkdir MyDrive
$ sudo mount --bind /media/pi/whatever-it-is MyDrive
Now, ~/MyDrive is mounted to the same underlying device as the thing under /media/pi. This works quite well for me.
GitD's list of things that are not ready for prime time:
2) 64 bit OSes
3) USB 3
Loves Linux; loves to dance.