Can we have multiple input and output section in logstash config file

This can be achieved fairly easy.

You can have multiple inputs with the same "type" e.g. jdbc.
just add those multiple times, is there a difference in the username you are using, or only the statement?

In the output box, you could do something like if "root" in jdbc_user { output 1 }
if the username is always the same I would go for a tagging, this would add an extra field to each of your line but, it will help you with the output. For each input you would need to add tags => "jdbc-1afterwards you can do the same thing in the output with if "jdbc-1" in [tags]