I am a newbie as well, but I can answer some of those questions - as I've done a lot of reading and youtubing :)

At this stage you want the tree to grow out as much as it can to thicken the trunk. In a bonsai pot, you are restricting the grown, which is good once you have a mature bonsai, but not good at this point. You might want to repot to a bigger pot or even plant in the ground for a couple of years until you get to your desired trunk thickness. A rule of thumb is the final height of the tree when in the bonsai stage should be 6-12 times the diameter of the tree. So if you want a 12 inch tree, you want the trunk diameter to be 1-2 inches. Let the apple tree grow out until its about 75% of your desired trunk thickness, then plant it into a bonsai pot. During this process you will need to let the tree grow as tall as it want too without cutting it back, which will promote the thickening of the trunk. Once you get to the desired thickness and it's ready for the bonsai pot, then you cut the tree back down to 1/3rd of the total high you want. You then let the tree grow out again and choose a branch at the 1/3rd distance to bee the first branch, and another branch to be the new leader (which will become the new section of the main trunk). This process will create taper and movement in the trunk, which is desirable. Another general rule is that you want your first branch at 1/3rd the total height, your 2nd branch at 1/3rd the remaining height, 3rd branch at 1/3 of the remaining height, etc.

As for soil, you want something that drains quickly, but retains moisture. Regular potting soil doesn't drain quickly enough, so you run the risk of root rot from the roots sitting in soggy soil for too long. A good bonsai soil consist of a mixture of organic and inorganic particles. You'll want to use gravel/course sand (for drainage and aeration), bark fines (for water retention and some nutrients), and a volcanic particle of some sort (for water retention, aeration, and drainage - like a combination of the best of organic and inorganic). Volcanic materials include akadama, lava rock, perlite, turface, and pumice. The ratio that you use depends on how often you want to water, how much it rains where you are, how hot your climate is, etc. Also, you are going to need to get a sieve and sift out all the very fine particles from your potting mix to ensure the drainage doesn't get clogged. Personally, my soil mix consist of 1 part turface, 1 part perlite, and 1 part miracle grow potting mix with all the small particles sifted out. I left out the gravel and used two volcanic-type particles as they offer the best benefit I feel. However, once I repot next year I will try 1 part pumice, 1 part lava rock, and 1 part bark fines to see how my plant like that mix.

I hope this helps!