"I want to know if you are free tomorrow."
Translation:Voglio sapere se sei libero domani.
They're not exactly the same. It's the difference between knowing a fact (sapere) and knowing a person (conoscere). http://my.lifeinitaly.com/threads/5171-conoscere-vs-sapere
Why sei and not the subjunctive sia. I tried sia and it said i used the io form sia instead of the tu form sei. This is nonsense, the subjunctive is the same for both is it not?
Conoscere is used for "know" in the sense of being acquainted with, as in, "I know her", "I know that city". Careful not to use "sapere" with persons, because that would mean you "know" them in a "biblical way".