I'm confused regarding how old my embryo is?

Go by the sonogram and what the doctor says. They measure certain things and are more experienced at detecting fetal age. You go by the 1st day of your last period but you may have ovulated sooner or later than expected and that would change the day you conceived a bit. Even if you have a due date of a certain day, it still could be a few weeks sooner or a week later so the date is just a guideline, not set in stone.