Having the GCP in preset mode seems like your best bet. Again, I don't have a GCP, but after taking a look at the GCP user manual, it looks like the GCP can still send program changes from the bottom 4 switches when in instant access mode. It does not look like you can use the instant access buttons to change presets on the MF, though. Or at least that's what I got out of it.
I believe Badmelonfarmer uses a GCP, so he'll know more than I do. In any case, the GCP user manual looks pretty thorough, so you'll be able to find a lot of answers there.
