Note: This is in the case when you are working on submodules.
If you change any file in the repos you need to commit the file again for that you could use:
git add <submodule-name>
git commit <submodule-name> -m"changed file"
This will allow you to commit only a subset of changes in that submodule and on a side note as @humblegumble answer says
git add -A
This is a good option to commit everything.
for changes goto that directory and use
git status
This helps you to see the changes done to sub-modules.
For more information please go through the link given below that helps you in understanding concepts of git