I suppose you mean a template you’ve created within the Manager of Modx.
This is stored in the database Modx uses, to be exact in the modx_site_templates table (if you’ve used modx_ as a prefix). Templates, documents, snippets etc. are not stored in folders on your harddisk or server, but in the database.
Css, images, etc. you can upload by ftp to any location you wish. Or to the appropriate folders you can find under /assets. In your template, just point to this location.
For example, if youv’e uploaded an image to /assets/images, you could use a html code in your template like this:
<img src="assets/images/image.jpg" alt="" />