For Paint, open issues/PRs on jspaint – unless they specifically relate to the integration with 98.js, in which case making the changes here is fine!
Generally open an issue (or comment on an issue if there's one already) before starting work on a PR, if you want the best chance of it being accepted. (I just don't want to see wasted effort!)
And opening lots of issues is fine! Please open separate issues for separate features/bugs/ideas.