The theme customiser will take the upload and put it in wp-content, but the folder or specific place is irrelevant. If you find yourself using it, you’ve made a mistake and your code has gone horribly wrong.
To be specific, your option is not referring to an image you uploaded, it is referring to an Attachment, specifically it saves the ID of an attachment.
Attachments are posts of post type ‘attachment’, they have post content, post parents, titles etc, and when you use the theme customiser to add an image upload the image gets uploaded, an attachment post will be created for it, and the ID of that attachment is then used to refer to the image. The ID is saved as a theme mod.
You can grab the various sizes of the attachment using functions such as wp_get_attachment_url
You can read more about this here:
http://codex.wordpress.org/Function_Reference/wp_get_attachment_url
You’ll also find the function get_theme_mod useful: