In short, you cannot have one git repo to be as sudirectory of another.
There is one exception to this rule: you can have one git repo as submodule of another, but this has a lot of limitations and inconveniences.
General approach to this is to have one master git repo which has no actual convent of its own, but only tracks few git repos as its submodules.
Alternatively, I would recommend using repo tool developed by Android project exactly for this purpose. It involves creating small git repository containing just one XML file (called manifest) which tracks where your sub-projects are checked out into and how they are glued together. This works really well on Linux and Mac, but unfortunately does not support Windows (repo requires symbolic link support by OS).
In certain sense, git submodules and android repo solve essentially same task, but using slightly different means.
