Ok, here's how I solved it. Deleted all the empty folders that should've been filled(Classes,cocos2d,scripting extensions)
I went to the project properties,source,and I added all of the above folders as linked folders. I then included the cocos2dx include folder and that was it.
It's a little bit weird since the first project I created,well... it did not require me to do this,but as long as it works,it's fine.