How can I position a logo
First of all, if you're going to change the theme, it is recommended to make a subtheme first so that updates don't clobber your changes. See Creating a sub-theme for more details.

As one option, the theme will have a page.tpl.php which is used to construct all the pages on your site. You could add your second image here.

Another way would be to add a block and place it in the footer if you really didn't want to modify the theme directly.