Hi Tracy - I have some good news for you. You count BOTH triples.
If you mean Triple WORD Squares, rather than Triple LETTER Squares, then what you have scored is called a 'triple-triple' (or a 'nine-timer', by some). It doesn't score SIX times the value of your play, but rather NINE times.
Why? Because a triple-triple is interpreted as 3x3 rather than 3+3. Triple-triples are the holy grail of Scrabble and the cause of those occasional mammoth record scores you hear about (200+ points for a single play, for example)