Custom Taxonomies

Can anyone teach me how to use the custom taxonomies?

Lets say I’m creating a post and want to put values a custom taxonomy named: taxonomy_menu-category with values: id,slug,title,desc,parent,postcount.

My question is how would I add values to them while creating a post.
I really have no idea how to do this,

Thanks in advance.

http://wordpress.org/plugins/json-api/