I loved reading Marrow and The Well of Stars and always felt like it was a trilogy. Is there a sequel? Is one planned?
I'm not sure if it's good or bad timing, but Robert Reed's website has just (April 20) posted a piece where he talks about what happened with the sequel, the vagaries of the publishing industry, and the future novels set in the Marrow universe that he's working on now. You might have missed it if you had only checked there initially and not also asked the question here (or if you went to the site right after it was suggested above).
If you're not already aware of it, his novelette "Hatch" in the anthology The New Space Opera (vol. 1) takes place quite some time after the events of The Well of Stars. It doesn't feature any of the characters from the books, it's about those trapped outside the hull.
As of date, there is no third book in this series. But, there is however more to read in the same universe. Marrow and The Well of Stars belong to the Great Ship universe as Robert Reed calls it. The following list is all his work in this universe, and the three last ones are forthcoming, the author has not said what these are.
[* Please note: The novella "Marrow" and the expanded novel Marrow differ dramatically. Readers should be aware that it is the novel Marrow that matches the continuity of later stories in this sequence.]