You get them to ramify by "waiting for three (3) years".

Then they will be 4-6 feet tall and not bonsai.

From my *very small* amount of experience with ginkgo seedlings, mine have only produced additional buds in their 3rd spring season. Mine are only grown in small pots or containers (not in ground which might cause faster growth), and every 2nd year seedling still only has a top bud. And I only have one 3rd year seedling. It's not much more than 12" tall.

Mine do not get tender loving care; often mis-treated, with pots overcrowded, no extra fertilizer, and only standard potting mix. (for now anyway)

Attaching a quick-not-the-best photo. You can only see three visible growth buds, but it has five total.

Photo 3rd year seedling:

I am not a bonsai person so feel free to take this with a grain of salt :-) But I do grow a lot of trees in containers, including ginkgo, and have for many years.

IME, ginkgo seedlings simply do not grow fast enough to be 4-6' tall after three years. Their rate of growth is considered 'slow' - especially in the first few years of life. And the process of growing trees on to gain some size and trunk diameter - and to start branching - before heavy bonsai pruning or training is very common. It is done with Japanese maples all the time.

This is completely off topic, but if I recall correctly ginkgo is dioecious, correct? So that means no nuts unfortunately. I don't know if you care OP, but if you're curious this article explains how to tell if your tree is male or female.

http://blog.pennlive.com/gardening/2012/08/ginkgo_gender.html

Unfortunately, these differences don't show up until the tree is about 30 years old.

Maximizing ramification is done via pinching, but first you need to have a trunk that's thick enough to be worthy of your efforts at bonsai. Ginkgos are most commonly grown in the "flame" style. http://www.why-bonsai.com/bonsai_history_ginkgo.html

Al