I am a senior undergraduate student and looking to apply to PhD programs. I am doubtful whether I should put my working papers on my CV alongside the already published works. I don't want to exclude them because I think my work in progress are more important than the published works. Will listing a separate section for working papers, with a side note on where do I intend to submit them be good?
Work in progress can be a good indicator of both interest and ability. I wouldn't exclude them and a separate section for it would be good. I doubt that a lot of undergraduates are in this position, though my perspective is the US.
Saying where you intend to submit/publish them is a bit speculative unless you have already published in those venues. But it is more likely to help than hurt as it shows you have a plan.
But in general, giving your work in progress shows an active research trajectory that might be carried directly into grad school if the circumstances are right.
I think this can be appropriate, especially as a student. When I was recently applying for academic jobs I listed a paper in my CV that was not yet published (or submitted at that time) because it was the main result of my dissertation.
Under my Research articles section I had two subsections: Publications, which listed papers actually published and Manuscripts in preparation. This allowed me to highlight some of my current and recent research.
I would advise you to keep the papers "in preparation" to at maximum a couple; I didn't include the half finished paper I wasn't going to submit for 6 months, or the ideas which I've written an abstract for, use this only for papers that are at least conceptually done. The reason for this is that you want to highlight them, and if someone asks about them they will be able to tell pretty quickly if the paper is still at the "idea" stage which would seem like you were padding your CV.