You question isn't specific to Git but applies to any version control system.
In general, it's a good idea to keep all of your project's assets (e.g. source code, documentation, scripts, binaries) in the same directory structure, where the different assets would be organized in subdirectories. That way when someone fetches the project from source control, they'd get everything that's related to that project without having to hunt down different pieces in other repositories.
When it comes to Git specifically, one consideration to make is whether your project has a lot of large binaries files (e.g. audio, video, raw images). Git's storage mechanism is, in fact, notoriously inefficient at handling big binaries that change often:
By default Git will compress and store all
subsequent full versions of the binary assets, which is obviously not
optimal if you have many.
If you need to store large binaries in your Git repository, you should consider looking at a Git extension called Git Large File Storage (LFS). Once this extension is installed, Git will store large binaries in a remote repository but still make it look like they're part of the local repository.