This message was posted on behalf of Intel Corporation
The IDEs supported by Edison are used to program in Arduino C++ (Arduino IDE), Node.JS (XDK), C++ and Java (System Studio), however, if you program directly on Linux, you have access to all of these (with the exception of Arduino C++) and pretty much any other programming language compatible with Linux not just Linux.
That being said, it comes down to your preference, I personally prefer using Linux directly, what I usually do is write the code in a text editor with programming syntax on my PC and then I copy it to my Edison to compile it. Nevertheless you might be more familiar to Eclipse, so you might be more comfortable using the System Studio.
Then my suggestion is that you try them and choose the one that you like the best.