You'll probably have to wait a while for complete guides to become available.
For now, I'll mention that files created in the external "resource collection" (also known as mode or just collection; roughly analogous to a "project") are guaranteed to go untouched by Ignition and will be treated as immutable. If you want to preconfigure/deploy gateways from source control, that's going to be your preferred avenue - essentially, duplicate the nested folder structure from
data/config/resources/core/
and manually repeat it in
data/config/resources/external/
for whatever resources you care about.
'Gateway configurations' is too broad - basically everything in the gateway is now captured in independent resource types, so you have to choose how selective (or not) you want to be when storing configuration to VCS. Images, for instance, are stored in data/config/resources/core/ignition/images.