I think keljonma posted a recipe for canning apple pie filling. I didn't add any thickener to mine. I figured I could add it at the time of baking. I haven't used my canned apples for pie yet though.
I made apple pie filling way back when I started canning. It seemed like an odd thing to can (to me) but I had apples, and I had a recipe. I don't remember using any thickener. What I do remember is that, when done, I had a number of jars of apple slices, all spiced and ready for pie ... but, when it came down to it, I don't make apple pie often, and really prefer using fresh apples anyway . I haven't done it since. I can apples as applesauce, as it is more useful to me than slices. I do dry a lot of apples though, and if I want to bake something with slices (and don't have fresh) I use them. I think that if I were to try canning apple slices again I would do them plain (unspiced) in a light syrup. But that is just me, and the way I cook/bake. I realize that having them all ready for pie might be very handy for others.
It's been several years since I've canned apple pie filling, but when I did I just mixed the apples with sugar & spices as if I were making a pie, but in mass quantity & heated it up in a pot, put it in quart jars & w/b for about 20 minutes or so. I never did use clear-jel. I wouldn't think you'd need to pressure can it if you are using tart apples & plenty of sugar....but that's just me so
When I used my filling for pie after it was baked the filling did turn out more like applesauce pie...not so many chunks & that's why I stopped canning it & usually now use fresh apples instead....but again, that's just me
You can pack them in syrup or water. Doesn't matter because they'll be cooked in the pie eventually. You can use cider, but it's basically just going to be a cloudy concentrated apple juice. You could also start with frozen apple juice concentrate, if you're feeling lazy or want it to be nice and clear.
I don't like the idea of using thickeners in anything that's canned...viscosity and all that. You can always add sugar and flour (or whatever) when you make the pie.