In a BOB trailer. When I tour with panniers I leave my trunk at home. This summer I'm bringing my BOB and this will be my trunk:
It locks, and I think it will be both squirrel and raccoon proof (not bear proof though.)
I've never used a BOB or a trunk, but I know people who have. I would say don't use the trunk or the BOB. BOB adds way too much weight, and a huge handlebarbag is good. They say that it's better to have more weight on the front than the back.