Just like your day pack, you can use plastic bags to line the inside of your duffel bag. Even if you have a waterproof duffel bag, you should create another waterproof lining to help combat the rain and elements.
I had a waterproof duffel, plastic bag linings, my clothes in individual plastic bags, and moisture and dirt still managed to slip in.

Tourists Skip Kenya, Head to Tanzania
Climb Kilimanjaro for The Children's Society
Mt. Kilimanjaro Forum Thread for the week of October 16, 2006
World Leaders Climb Kilimanjaro
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