Thank you for your response! This definitely seems like it's on the right track of what i'm looking to do.
I guess to elaborate on my original question:
Which folders included in the IoT Dev Kit extracted files are the key files that give the Intel IoT Edition of Eclipse the added functionality and which ones are simply the basic Eclipse resource files? Should I just be looking to merge everything except for the folder named "eclipse-win" or are there Intel specific resources like plugins that exist in the "eclipse-win" folder as well?
I'll edit my original post to include this information which I should have included previously but i'm currently using Eclipse Mars 4.5.1 C/C++.
I found that in Intel® Edison Native Applications Guide, specifically in section 3 it is explained how to set up the Yocto plugin on Eclipse, why don't you check out this document? Let us know if it helps.