How dependent are stylus devices on software?

I am considering acquiring a tablet or phablet with integrated stylus. One of the first things I expect to do with is flashing the latest vanilla Android release. That done, is the stylus expected to work properly? Can I then install alternative note taking programmes (e.g. [Quill](https://code.google.com/p/android-quill/)) ? Or is the stylus functionality fully dependent on vendor software?