You can put the apple butter in the fridge for a couple of days if needed, then just warm it back up to a full boil on the stove when you are ready to can it. Remember - "hot into hot" when putting something into a jar for canning. Never put cold stuff into a hot jar.
The clear jell is the thickener for the apple pie filling. I can't find it anywhere but on-line. According to the USDA, it is the only thickener that is heat stable and approved for canning. Some people will use cornstarch and/or flour as a substitute - I have seen 2 two different fails when using those. One got really yucky-clumpy-gooey and the otherwas that the thickener lost its thickening ability and the pie filling came out soupy (almost slimy like) after a couple of months on the shelf.
I used a recipe that I got off of this thread a couple of years ago - it is not USDA approved, but it was really good. It used tapioca for the thickener. (post #7832) Tapioca was what my grandma's recipe called for.
You could also mix everything together without the thickener and can it with a little liquid (apple juice). When you want to make a pie, strain the juice into a pan, stir in cornstarch and thicken it on the stove top while you make the pie crust. Add the apples that you strained out and put into the pie shell and bake as usual. Alot more work than just plopping into the pie shell right out of the jar, but it works if that's all you got. You end up with more suace this way also. I canned some sliced apples in straight apple juice and made a pie filling by adding cornstarch and spices so I could make some appetizers for a party out of canned apples and won-ton skins. It turned out good that way also.
Edited to add - if you can in just juice and thicken everything all together later, the apples may become over cooked. That is why I say to drain out the juice and thicken just that by itself before adding the apples back into the juice. Otherwise you will end up with applesauce pie.