Usually, they calculate it from the first day of your last period, not the actual day of relation. But your doctor can tell you more accurately through the dating scan.
I used to break my head trying to calculate the exact day of conception! Honestly, don't worry about the exact date, the doctor's ultrasound scan is the most accurate anyway.
I am also confused about this because my period cycle was irregular. Did your doctor give you a dating scan yet? That really helped clear my confusion.