I'm looking to create a parent customer that has child customers underneath it. So for example Home Depot as the parent and store #300 as the child.
Yes it is possible. You need to however identify what is different between the stores and what information you'd like to have available for each store.
1st thing you can do is to create a master catalog which will be managed by parent and then create a virtual catalog for a child. Then create two stores, one for parent and one for child (assigning appropriate catalogs for each). This will allow you to control which products are available in which store and also control taxonomy (categorization) for each store.
You can also control security for each store using organizational structure. For instance if it is a B2B solution, you can create organizational structure where parent organization is Home Depot while child organization is your store. Now all employees from child org will belong to that child org and can have limited set of permissions.
Another possibility is if you want to manage inventory differently for each store. In that case you will need to create fulfillment centers and assign them to a specific store. That way product can be made available in one store and not in the other.