I'm responding to you via the forum as I've just seen your email in the helpdesk with the attached screenshot.
The boxes will be center aligned by default on the page, as long as you have the correct amount of boxes for the set selected in the page meta then they will space out accordingly. In the page meta you'll see an option for selecting the number of boxes per row and another per page. Make sure the per row option is set to reflect the amount you actually have on the page, then the spacing will be correct.
Other things that could affect the layout and alignment of the boxes would be if you've entered any custom css which has shifted the main margins/padding of the page container.
To see more on the box settings options please check -
From looking at the screenshot its hard to tell what exactly could be causing it without a live link to the site where we can check the code, look into the padding/margins etc, but they'd be the first things I'd check.