I'm using https://github.com/AtomLinter/linter-jscs. The docs say:
It will lint on edit and/or on save
It seems that it lints on edit and save all the time. I don't see a way to configure it to lint on only save.
First of all you really should be looking into moving to ESLint (linter-eslint) as all development on JSCS has stopped.
As for your question, you can configure this behavior in the Linter package by disabling On-the-fly linting there. This package is simply a service provider allowing linting of code through JSCS, the Linter package is what controls when it is ran, and how its results are displayed to the user.