Hi
As soon as the seedling is large enough to handle you can transplant it into a bonsai pot, this will help to keep the plant small.
The pruning of roots and the time of year to prune can vary depending on the species you are growing, same with the pruning of the branches.
There are some good books on Bonsai available at the library, which goes into detail about the species, when to prune etc.
It is certainly worth you having a read of the types of bonsai you can grow, and how robust they are.
It is indeed a very rewarding hobby, especially watching it grow into a bonsai, to the shape you created, you just need time and patients.
If you go onto my website, there is a Bonsai/Tree Category, where you will find pictures and a description of them which is worth a browse
SEEDSENSE