Perhaps others can give you specific advice on how to winterize your tree, but here are some thoughts:

Apple root balls get big. If you're planning to have this thing in a pot for a couple years before you move, you'll need a big pot eventually, no? Maybe moreso since the roots will be those of a standard apple (not sure on this point, though).

Those I've known who keep fruit trees in pots usually have dwarf trees. A lot of people will say, "you can make any tree any size by pruning," but it seems to me you'll still have the vigorous roots to contend with.

People keep all sorts of plants heeled in all winter long. I briefly considered heeling in some seedlings in the bed for the winter before planting them out next spring (I gave up this plan to encourage better root growth). Except for heeling them in, I wouldn't have winterized them in any way. In your climate, maybe things are different, but if I were you, I'd just leave them heeled in. Maybe consider trunk protection (hardware cloth or something) to keep the critters from munching on/girdling your tree under that foot of snow.

I've never espaliered fruit trees. I wonder if it's easier/better with dwarf/semi-dwarf rootstock.

My dad planted apple trees everywhere he lived and always said he was happy to leave them for future owners to enjoy when he moved. Maybe you just want to plant it and be done? Maybe graft on some edible fruit so that people are more inclined to keep it. :) Anyway, good luck!

It's not really what you asked, but I am suprised that it is still so small.
I started some seeds in this spring 2012 and they are about two feet tall.

Sam_NY - I'm not sure how big the root ball will get, I'll have to look into that. Next spring, I was thinking of repotting it - but if it's already running out of space, maybe I'll have to consider leaving it for whoever buys our house :).

I had thought about covering it with a rose cone for the winter - but maybe just wrapping it in some burlap will be enough to protect it for the winter.

I like the idea of grafting on edible fruit later on - do you know if some fruits are better than others? Should I just make sure to pick ones that are suited to my zone?

daemon2525 - I was wondering if it was growing as much as it should. I think I unintentionally pruned it at the top of the trunk - that is, when I pulled it out of the garage, it didn't grow from the top anymore. It just started growing new branches vigorously.

Have you fertilized your seedlings at all? I've read not to do that before the winter, but I may give it some fertilizer next spring. And I may have watered it too much this past summer, almost every day in July (thankfully, it was a pretty dry summer, pretty much no rain all of July).

Thanks for the help!

All I did to mine was put some leaves around the roots, about 2 inches. The thing is exposed to the north, and survived no problem.

Ill see how well it does this year.

Good luck.

Unless you're growing in a greenhouse I think it's wise to grow fruit suited to your climate. (see http://forums2.gardenweb.com/forums/load/fruit/msg0921115727022.html?4)

You're pretty limited to grafting other apple varieties (I've heard of people grafting pears on apple roots, though I think that's likelier to fail). Maybe there are some exotic apple relatives that would work. I've only ever done apples to apples, as it were. A little web research will yield some interesting ideas for apples suited to your zone that you can try.

Just curious: do you happen to know whether the seed you planted came from an apple grown near you? If it came from, say, Australia, I could imagine the genetics working against you up north.