I've received differing answers from many people on this. I'm proposing a planetary atmospheres project and while I'm submitting it to Geosciences - Climate Dynamics, I'll also probably include "Physics and Astronomy - Astronomy" and "Physics and Astronomy - Theoretical Physics" as part of the "% of program for Primary Field of Study". I'm in a geoscience department, but my adviser is a theoretical physicist and I come from an Astrophysics background. I'm slightly hesitant about including panels beyond geoscience though, since the physics/astronomy applicant pool is far stronger than the geoscience applicant pool, and there may be much bigger expectations expected from people in physics/astronomy.
One person told me that they might just average the scores of the reviews from both panels, while someone else told me that it can't hurt at all.
Is your proposed graduate program interdisciplinary?
Note: Interdisciplinary research is defined as a mode of research by teams or individuals that integrates information, data, techniques, tools, perspectives, concepts, and/or theories from two or more disciplines or bodies of specialized knowledge to advance fundamental understanding or to solve problems whose solutions are beyond the scope of a single discipline or area of research practice. Please provide an estimate of the balance among the Fields of Study represented.
According to the NFS
Your application will be assigned to the field of study you list first in the Proposed Graduate Program section. ... Therefore, you should choose which field you list first carefully, with consideration of which panel has the most appropriate component fields. ... All interdisciplinary applications are clearly marked as such during the review process. Many panelists have interdisciplinary expertise and are capable of evaluating interdisciplinary applications. Additionally, if necessary, the panel can transfer your application to another panel for either a full review or for commentary and feedback.
While in some cases they might average the scores, this does not appear to be a requirement. I would suspect that in most cases they would do the review within a single panel and rate you accordingly and only seek expertise outside the panel if absolutely necessary.