this is where you may lack understanding! A vocabulary that is set up in admin categories holds a set of taxonomy terms like pants, type, boy girl. Then you tell Drupal what nodes (better node types) like page, story, product can get tagged with one or more of them.

so, what you want is not a taxonomy term pants, since you want boy-pants and girl pants, right? Good.

So you do now want to go for pants showing boy and girl pants ...

Thus you create a taxonomy tree that hold different pants meaning each human term pants gets a different tax id below since it belongs to a different branch of the overall tree of the vocabulary! Pants are not pants...

Therefore you create a vocabulary that has as levels of depth thus you tell drupal that it is no simple one, a click in the edit section of the category "shop tags" for example..

The point being is when you now add tax terms to your vocabulary it asks you where it is to be placed like in menu tree. Then you YES name twice the teram pants, but once you put it under boys and the second time under girls. The breadcrumb path above the product on display then shows you, like this boys - pants - XXL - By Lewis.
You folks then click on a tax path links as above and just get what you want them to see..