The thin trunk of seedling junipers will not thicken much once they are out of the ground (in a shallow pot). So, to keep things in scale, the height of the plant will need to be kept short (@6 inches) if it is to give the miniature impression of a tree. Tiny bonsai often have to be more impressionistic rather than exacting in branch placement. If you are aiming for the look of a cute evergreen shrub in a pot, it could be allowed to grow up and out more, about like it is. To thicken the trunk and then develop a medium size bonsai, juniper seedlings/saplings will need to be growing back in the ground for 5 or ten more years (and likely with occasional root pruning to avoid leggy roots). Or just buy one which the landscape nursery or bonsai nursery allowed to grow larger prior to digging and selling. Find pictures of a juniper bonsai you like, and then compare the thickness of the trunk to the height of the tree. After your recent root work, do not put it outside until danger of freezing is gone, but then a juniper needs to be outside constantly except for the occasional showing. Your juniper does look green and healthy in the pictures, have fun, welcome to bonsai.