This is an excellent question with no easy answer. Drosophila is one model organism for which we know something about how expression of specific genes leads to developmental structure [1] but there is a lot still unknown, not just for Drosophila but also for cellular differentiation [2] more generally.

[1]: https://en.wikipedia.org/wiki/Drosophila_embryogenesis

[2]: https://en.wikipedia.org/wiki/Cellular_differentiation

Basically, the mother determines which side of the egg is "up" by adding chemicals to one side. From there on many different gradients of proteins and chemicals form, which pattern embryos into subsections of more and more detail. The graphics in the Drosophila article linked in the sibling will give you a good idea.