WordPress's XMLRPC interface doesn't provide a mechanism for reading or writing custom fields on a post.
I chatted with Joseph Scott and Westi a bit about this, and there is some debate about whether the custom fields should be included in the body of the post for new/edit/getRecent posts, or whether there should be a separate API.
It seems like it would be tedious to have to explicitly ask for and set the custom fields separately from the main get/set APIs, but I would be happy to see support for it in one way or another. Right now there's no way for custom clients like MarsEdit to support this feature.
Daniel