For examples on how to work with on-premises Skype for Business using scripts, have a look at the following scripts from our repository: https://www.adaxes.com/script-repository.htm?cat=22. As you can see, in certain cases, it can be done without importing Skype modules.
Additionally, it is not necessary to use scripts to enable/disable users for Skype for Business in Adaxes. To do that upon user creation, you can use the built-in Enable or disable for Skype for Business action in a Business Rule triggering After creating a user. For details on automating user provisioning, have a look at the following tutorial: https://www.adaxes.com/tutorials_AutomatingDailyTasks_AutomateUserProvisioning.htm.
If you still need to use scripts and specific Skype PowerShell modules, you need to install the modules on the computer where Adaxes service is running (if you have multiple instances of Adaxes service sharing common configuration, install the module on each computer where the services run) and make sure that the Adaxes service account (specified during Adaxes installation) can access the modules. Should you have issues with the scripts, please, provide us with all the possible details on the desired behavior with live examples.