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I know I am crazy to try Bonsai from scratch but I hope I live long enough to see them grow into something.
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At least you're admitting it. Growing bonsai from seed can be a very rewarding prospect, but its also a very long and difficult road. Its actually easier to start learning on nursery stock than to try to learn bonsai by starting from seed. Working with older material helps you develop an 'eye' for trunk lines, movement and etc. - which is all stuff that you are controlling from the start when you're working with seedlings. If you do not feel comfortable in your design skills, its hard to start a design from scratch (i.e. start a bonsai from seed).
First off - I would not do anything with your seedlings right now. Its fall, and they are storing reserves and setting their buds for next year. You do not want to do anything that will encourage new growth right now, since that new growth will not have time to harden before the frosts come. In the spring, I would transplant things to a sunnier spot and let them grow. JL has a good timeline that you can follow for development. Unfortunately - if you want thick trunks, you need to let the trees grow wild. Two years ago in the spring I had a 6' (foot) tall trident that I cut back to 6" (inches), which will eventually be a tree with a finished height of around 10". To get the size trunk that I wanted for the 10" tall tree - I needed to let the material get 6' tall. Its almost two feet tall again, but that is because I need that wild growth to callous over the large wound from cutting it - I did very little to the tree this year and last year, since I needed all its growth for wound healing. I may or may not make my next cut next spring - it depends on how the callous looks when I put the tree away this winter. It might need a third year of healing before I can make another big cut and then start on its branch development. Yes, the trunk would heal over eventually even if I made the next cut - but the more time I give it to recover from each step, the better the finished tree will look - wounds heal much slower when the growth of a tree is constrained, or stressed - such as major stylings/prunings.
-Centaura