How to setup your account
Organizations contain Spaces, user groups and users.
Organizations are a way for your account to be in multiple contexts, for example if you might have multiple companies. They are not a way for you to group users in 1 company.
User groups are a way to group users in 1 company, e.g. your departments. User groups allow you to assign access policies to certain Spaces so that only some users are able to see or edit content.
Do not use Organizations as a way to group members of the same company
This will work against you. Search works at Organization level, thus you will not be able to search for information in all your Organizations. It's also not possible to mention people & docs from other Organizations as mentions and docs are at the Organizations level as well.
Spaces are a way to group documents. They are similar to projects in your company. They can be assigned access policies so that only certain groups of people.
Users are members of 1 company.