From this hackspire page I see that programs can be built and debugged from Eclipse. However, when I import my project and build it, it uses GCC instead of nspire-gcc. Is it reading my previous makefile at all? How is this fixed?

Edit: Eclipse also can't find os.h, although [ndless directory]/sdk/include is in the path.

Are you using Windows? I had that problem in the Linux version of Eclipse, and I (reluctantly) installed the Windows version. The Windows one works fine for me. Go to Properties>C/C++ Build>Tool Chain Editor and make sure the toolchain is "No Toolchain," and the builder is "GNU Make Builder." (Those are my settings, at least) Also, make sure EVERY folder in the sdk directory of Ndless is in your PATH variable. (sdk/bin, sdk/include, sdk/lib, and sdk/system) Some of these things might not be necessary, but this is how I got my system to work.

This youtube video from ExtendeD really helps. MAKE SURE TO TURN CC ON, as that's how the instructions are given!

Edit: Make sure to go to PROPERTIES (from the project explorer window, then right click on your project name), not PREFERENCES.