We utilize Kaseya and Autotask. Currently I have agents that alert for Critical, Error, etc. Obviously this creates tons of duplicate tickets created in autotask. My question is how do we get the duplicates to just update the same ticket until a technician fixes the issue, ie. closes the ticket?
That sounds to me like you do not have the "Ticket Request De-dup" procedure properly configured in service desk (assuming you are using service desk for ticket generation) If you're using the legacy ticketing configuration, I would recommend looking at kaseya service desk for that functionality.
I can recommend this product: automationexchange.kaseya.com/.../62
It integrates Kaseya ServiceDesk and AutoTask.