GMS 2 Source Control should I use internal or GHDesktop?

So my team has expanded to 3 people. And on my first merge I spent the better half of a day fixing conflicts on the new branch. I was able to get everything cleaned up by the use of SourceTree and GitHub Desktop. SourceTree has a conflict editor built in. My question is how good is the built-in SCM tool in GMS2? Does it ignore things like the ide settings between engineers do it just capture all of that as well? Also how well does it handle conflicts? I know the conflicts can be minimized by me having my team work "further apart" I am working on that. Anyways anyone ever uses the internal GMS Source code manager with GitHub?