Spanning Backup for Office 365 offers a public API, in which you can automate license assignment.
If you have a large number of Spanning licenses to assign at once, using PowerShell to assign user in batches using CSV files*, or, make AzureAD calls and enable users directly based on OUs or other metrics.
Spanning has an unofficial example PowerShell module that you can use to complete this process, which can be found here. Additionally, please watch this instructional video which details how to use this example PowerShell module.
Note, this module is not directly supported by Spanning. If you have issues using the script, please log an issue on the project page linked here above.
*Spanning recommends enabling users in O365 in batches of 250-500 per day to avoid becoming throttled by Microsoft. Monitor users for initial backup completion before enabling more. Enabling significant number of users concurrently for initial on-boarding also works fine, but may result in extended backup times due to API throttles Microsoft enforces from their end spanning cannot control.
If you have any additional questions, please contact Spanning Support - we're always happy to help!