Today, someone asked me how can one tell whether their child is simply a cisgender girl who doesn't want to conform to gender expectations or if that child who is assumed to be a girl (because of their genitalia) is actually not a girl. This is what I had to say about that:
First of all, no child's sex is the same as their gender. Gender and sex are entirely separate things. Secondly, there's no such thing as a "cis-gendered girl". It's the equivalent of saying someone is a Mexicaned girl or a Blacked girl or a Indianed girl. The term is "cis-gender/cisgender". To answer your question, you know the difference between a cisgender girl rejecting gender expectations and a child who is not a girl (even though some people may assume that they/he/ze is one) by actually talking to your child.
Being Creoles from the American South, there's a real bourgeoisie streak that dictates that women and girls should wear their hair long (and preferably straight). The girls certainly don't engage in sports that might result in scratches or scars on their skin. And make-up is de rigeur no matter where you're going. And, in my family and the religion that most of us practiced back then, women and girls ALWAYS wore skirts or dresses to church.
Despite that, I come from a family where there are many women with careers in the sciences. We tend to be very good at math, too. My aunt and my cousin (who is a girl) happen to be the best football players in our family. I've seen both of them tackle and plow through men like a knife through butter. We strongly believe in finding out and nurturing each child's gift or particular talent. So, regardless of their genitalia, we expose our kids to lots of activities from very young. I'm disabled, so I couldn't do it with hir, but my child went camping and hiking with friends. Ze was a member of a mixed gender scouting troop. Ze got sewing lessons from one grandmother and agricultural experience with one of hir grandfathers. Another of her grandmothers introduced hir to the magic of cosmetics (which my child promptly used as face paint and made hirself look like different animals). Ze got art lessons from hir bio-dad and math enrichment from her step-dad. Ze spent a lot of time with hir friend's mom who is an entomologist.
In other words, we never taught or allowed hir to believe that certain genders aren't allowed to pursue certain paths. By the time ze was 5 years old, we no longer even practiced a religion that had clothing expectations for certain genders. As an aside, I personally believe that children should be taught ethics, not religion, so it wasn't a problem for us dealing with what some faith tradition expected "girls or boys" to do and be.
In an environment where children are free to pursue their interests and not shamed into rejecting something they love, they can feel fairly comfortable making their identities clear. My child didn't have to worry that not being a girl would ruin some grand scheme that I had planned for hir future. Ze still loves marine biology, is good in math, majors in Fine Arts, wears make-up, shops in the boy's section of the department stores (ze says that's where ze finds the best shirts), has a hairstyle that is considered masculine in this culture, dates people of all genders, and still sits on my lap every chance ze gets! Ze is completely comfortable with the body ze has. Some trans* or gender variant people do experience dysphoria, but others are just fine with their bodies. They don't need certain parts in order to be the gender they claim. My child knows ze's bigender in the same way that you know you're cisgender.