I am not sure if there is a better way. Here is what I do, e.g. in calculus classes where they have to sketch some graphs once, but the rest of the semester is completely on-line. I edit the problem so that to indicate at the very end "Now sketch the graph of this function and turn it in on such and such date. The graph is worth so many points." Then I grade the paper part separately. WeBWorK shows only how much the on-line part of the question is worth, but I explain to the students in advance that this homework also contains a paper part.
If anybody knows a better way to grade such assignments, I'd be interested too.