The Rambam gives very definite guidelines as to how we are to know which Mitzvot are part of the 613 and which are not. He claims that there is great ignorance regarding the way to categorize the various commandments. One such mistake comes from the specific blessings known as ברכות המצוות. It is only logical to assume that if a ברכה begins with the words, אשר קדשנו במצוותיו, where we bless Hashem for sanctifying us with His Mitzvot, that we are speaking of a Torah Mitzva and one of the 613. This is not always the case. For example, we use this format for saying Hallel or lighting Shabbat candles or Chanukah candles or reading the Megillah on Purim. We even use it when we wash our hands. All of these are rabbinical laws but we say אשר קדשנו במצוותיו, because we are following the Torah commandment to listen to the teachings of the rabbis. Being able to properly organize and categorize is important for us to be able to know how to prioritize the various Mitzvot.