Which file should my style be in I'm putting this question in the Drupal forum rather than a CSS forum as I don't know if I just have a CSS issue or if the issue is more Drupal, maybe how I'm using the .info file.

I'm using Drupal 7 with UberCart and the AT Commerce sub-theme of Adaptivethemes.
If I put my CSS in styles.base.css they take effect. However, it I put my CSS in a separate CSS then they do not.

I edited at_commerce.info so I have this

// CSS
stylesheets[all][] = css/styles.custom.css
stylesheets[all][] = css/styles.base.css
stylesheets[all][] = css/styles.modules.css
stylesheets[all][] = css/styles.settings.css
stylesheets[all][] = color/colors.css
stylesheets[all][] = css/uc_product.css


I tried styles.custom.css as the first in the list as shown above and the last in the list and it make no difference. styles.custom.css is empty except for the 2 styles I'm trying to put there. When I put the 2 styles in styles.base.css I am putting them at the bottom of the file.
Just to eliminate a possible cause of your problem: if you have enabled CSS aggregation then you must clear the cache before changes to CSS files become active.