How can I determine the source of a basement flood?
If it was a sewer back up you can install a check valve on your waste line, these need to be accessible as they require maintenance but will prevent the sewer system from backing up. Floor drains &amp; showers are the first to flood in a back up but then toilets and washing machines, sinks all become possibilities.  

Depending on the type of condensate line moving the trap higher may be the only safe method as check valves on condensate lines tend to fail. 
Other than monitoring and identifying the water entrance point it may be hard to figure out, if the sewer was backed up and your sump pumps into it, where would the water go? Could the pump itself not only have been overwhelmed but provided a path for water ingress (if their is not a check valve in the pump).  I have seen sewers back up and put several feet of water in a basement with the water appearing to be clean.