I would like to update SalesTaxII rates and the program while users are in the system.
Technically, it could be possible for someone to have a lock on a record that was being updated by the monthly update process. However, in reality this is highly unlikely. The user would have to be in rate maintenance (an option customers should never use without being under Avalara instruction) and they would have to have the actual record open that was being updated by the monthly update. Since there can be up to 68000 records in the tax database and a monthly update usually only updates between 5 and 50 of those records, then chances of a conflict are almost non-existent.
So, in reality, you can run the update at anytime, even with users on. However, Avalara always recommends performing the update at a quiet time. Many users create a CL program and run it from the job scheduler at night.