you can delete it and then your index file will be used, or try editing the md file. Depends on what you are trying to do.
If you are doing the default jekyll new site, I believe it is using a gem theme which hides a lot of stuff from you, make sure you read everything on that link.
I have not watched the latest video serious made by giraffe academy but have you seen them? they look new so they may be more helpful than some of the older stufff - though some of those are excellent.