Oh be sure to mark it after you baste it. I always feel like the quilt top is such a delicate thing. Once you have it basted it will start to feel like a real quilt, and will be more stable for all of your marks. :D Also with it being chalk you might smudge it when you're basting.
If it were me I'd do the outlines first too, so that the borders will stand out, but that's up to you because I don't think it will make much difference in the long run.
I've never heard of the Clover Pen, I use something different (that one of these days I will write a review on) but it should work fine, just be sure to read ALL of the print on the package.