As an Administrator take the time needed to create a good active directory structure. This will definately save time and frustration. Remember these are the bones of Active Directory and deserve the attention.
What works for me is to break up the structure into individual OU’s. This makes it easier to navigate and easier to apply group policies too.
Do yourself a favour and create a Test OU, this will help to test policies, test Permissions before actually putting them into place to make sure they work correctly and apply to users correctly as well.