Your stove will be fine, wherever you leave it. ...well, maybe not stuffed inside the sleeping bag. As long as all the food and smellies are packed inside the canister, and that is placed away from the tent a few feet, everything should be ok.
Marmots chew into packs and tents if they smell food (or food spills) inside. Your tarp tent doesn't close up, so all should be fine. Don't wrap anything up -- if something smells good, they might chew. Leave the pack zippers open, too.
