Can you bypass the initial script in a custom SQL/SWQL query when creating an alert?

I am trying to create a custom alert built around a database query that uses 3 custom pollers. A couple of the pollers stores the results in the same table and column so alias are used.The query pulls all the necessary information but i cannot get the alert to trigger correctly. I believe it is due to the fact i cannot use my select statement as Solarwinds inserts its own select statement.