I can't see any problem listed in your post. Do you simply want to turn off the low disk space message? Or did you try to install a large program and received this message?
I purchased an external 232gb hard drive some back. It runs fine. I don't understand the interaction between the external (e) drive and my internal (c) drive. My (c) drive has 15.7gb used and 2.8gb available. My purchase of the external drive was to have abundant hard drive capacity. I've already received a message that I didn't have enough room on my (c) drive. Any thoughts would be appreciated.