ITA Matrix isn’t some magic tool that will miraculously give you cheaper flights.
It’s just a search engine that has more options than others.
You can define things “I want to fly from Boston to Malta via Newark on a combination of United and Lufthansa, and I don’t want the connection time to be longer than 3 hours”..
Or you can say “I want to fly somewhere on Iberia from Madrid, but it has to be on an A330 or A340”.
Give us some examples and I’m sure someone can explain to you how to search for it.