Indeed, conditions can change in an instant. I forget what lake it was - maybe Rove or Watap, but the cliffs and the sudden wind put us in an unexpected wind tunnel, with no place to shelter. It took a lot of hard paddling before we got to a cove where we could wait out the wind. Also, a novice companion, or complacency, can put you in the drink pretty quickly. Regardless, before you 'go live' in cold weather, you should practice swamping in controlled waters. Use your drybags or duffelbags or other containers, put some duct-taped PVC in your bow case to simulate your bow, whatever, and stress-test your setup. If something isn't going to work, figure it out in the daylight before you find yourself trying to outrace a storm at dusk.
On that note - keep a spare, waterproof headlamp in your life vest, and put some retroreflective tape on any item you that's important enough to swim after in the dark.
I've got a SeaLine portage pack that is awesome, and is my go-to BWCA pack, but it's a bit spendy if you're not committed to paddling. Cheaper Coleman drybags from Walmart or Dunham's or whatever are in most casual budgets, and you can probably fit 2 or 3 in a seabag if you're going to portage them anywhere. Which, for most of us paddling to a hunting spot, we won't be portaging, but they're still handy to manage stuff in the parking lot. Put your retroreflective tape on both the seabag and the drybag. The cheap Coleman drybags secure with Fastex buckles, so you can clip them around your thwart, which will keep them from floating away. Get 2 more than you think you need, they fill up pretty quickly.
But I'm chasing squirrels. You're asking about putting a JX3 and your gear and your bow in a fiberglass canoe. If you have traditional seats, sit in the bow facing rear, as suggested above, and put your gear in the 'bow'. Put your gear in dry bags and wedge them in place, lash them in with bungees. Your empty pack can get bungeed to the drybags if it won't go inside. Bungee your JX3 to the seat so that it can't damage the hull - I think the whale tail is the only part that might cause damage. I'm used to Kevlar canoes which are a bit more delicate. If you're going to skip that and wear a soft saddle, put it and all your climbing gear in a drybag.
Regarding your bow, it depends on what case you have. If you have a watertight case like an SKB, bring it in the case. I don't expect you to portage it anywhere - that would be an awkward hassle - but it's probably worth bringing a ghillie blanket and hiding it a few dozen yards away from your canoe to hide it from thieves. If you have a non-watertight foam-lined clamshell case - like I do - use a soft case instead, and bungee it to a thwart or seat as far forward as you can. Taking an archery shot from a bobbing canoe is easier said than done so keep it secured. Generally you want all the weight in the bottom of the boat to prevent it getting topheavy and tippy, but a bow in a soft case is pretty light, so put it where it won't get damaged. Probably worth putting some cut-up pool noodles in or lashed to your soft case as insurance against sinkage.
