Do grad schools look at the overall GPA in applications, or do they look at particular courses?
If this is the US, then it could be either, but the grades that are most important are the ones that relate to your background and aptitude for the program you apply to. Some others may also be weighted fairly heavily. For example, if you apply in CS, then your grades in a writing course might be considered significant, since writing is an important part of CS overall. 

So, what is relevant and what is not depends on a lot of factors and is probably judged a bit differently by everyone who reads your application. But think broadly about relevance. Just because it isn't your major subject doesn't mean it is not valuable. 

But, there is no reason I can see for you to avoid applying now but using additional coursework as a backup. You don't really know how acceptable you are until you get the application in front of some committees. And their view will depend on much more than a few numbers such as your GPA. Letters of recommendation, especially. 

The view outside the US might be a bit different.