Hi Stef,
The main call for style.css in header.php and this file name should only exists the once, and does not need the file name:
<link rel="stylesheet" type="text/css" media="all" href="<?php bloginfo( 'stylesheet_url' ); ?>" />
Not sure what you mean by two URL's, do you mean you have two files?
If you do the second file should not start with style and you can call it like this, UNTESTED code:
If you had a second stylesheet in a subfolder /styles/ in a parent theme:
<link rel="stylesheet" type="text/css" href="<?php echo get_template_directory_uri() .'/styles/custom.css"'; ?> media="all" />
If you use a child theme and had a second stylesheet in a subfolder /styles/ in a child theme:
<link rel="stylesheet" type="text/css" href="<?php echo get_stylesheet_directory_uri() .'/styles/custom.css"'; ?> media="all" />
HTH
David