I'm sorry but I still don't understand what the problem is. I learned that the files with the tilde at the end are just backup files and can be deleted easily. The file (host.c) without the tilde has the modified number of cores (1) but when I run the mandelbrot program, the speed and graphics haven't changed at all.
Sorry, I'm new to Parallella and Linux in general. Thanks a bunch for helping me out.