I am trying

I am trying to minificate my website to improve server response time, however whenever I run the test with Hummingbird I don't know how to go through each file to see which will cause an issue with my website. I went with the include/exclude button to go through each file, but it seems that everytime I hit Save Changes, my website is messed up again. How do i go through this process to actually minify these files?