How do I update dependencies and do I need to?

Hello. I’m not a master in any of this. When I was making my website, I just cloned a jekyll template on the website version of github and began changing it and everything - I tried using github desktop but it’s an absolute utter rocket science for someone like me, it seems. I cannot even connect the repositories I have on the site with what’s in the desktop version - every time I try to clone my website repository, it just clones the first repository it gets its hands on and not the one I need. So how do I update them the dependencies, and do I have to — as github suggests?