I'm happy to help you with any questions concerning Scope Management. Generally Scope Management is not a factor unless additional Application Servers have been implemented, and those scopes are only needed on a secondary application server (not already defined on the primary). Common instances of this scenario occur where orgUnits or Computer need to be specially managed at the secondary app server.
In the case where you are exceeding your licensing limits, more often than not this is traceable to one or more WMI-based tasks that are being targeted to a larger group of systems than is necessary. However, in order to target a task to an orgUnit, first the Domain containing the orgUnit must be defined as a managed object in an existing management group. If you do not have a defined DOMAIN in your management group, then the key will be finding which tasks are contributing and how they are being targeted.
Given that a ConfigMgr AD Discovery task will populate many collections with all domain computer objects found, it's quite possible that a task has been targeted to a ConfigMgr collection -- such as All Systems -- and this is accounting for the excess number of systems in your counts. If the intent is to manage PCs only in specific orgUnits, but you do not have a defined Domain, then this would involve defining custom ConfigMgr Collections which contain only those desired PCs.
Alternatively, you will need to add the DOMAIN to the management group, and then you will be able to target tasks to a specific orgUnit.
For assistance in reducing your counts, reviewing your Task History, removing Scheduled Tasks that may be contributing, or configuring your management group, please use the SolarWinds Customer Portal to submit a technical support ticket.