Here's a detailed explanation on logo placement:
First, group all the logo elements together (text and symbol), then completely center this group of elements in the artboard using Illustrator's alignment tools (Align to Artboard, then center vertically and horizontally, placement at exactly x=1000px and y=1000px of the artboard).
Then, resize the entire logo from its center. the entire logo must be as big as possible, touching, but not exceeding the margin/guide.
Depending on the proportions of the logo, the symbol or the text will touch the margin/guide in one or more places, but not necessarily more than one place. This means that sometimes, only the text will touch the margin/guide and other times, only the symbol/icon will touch it.
The template file includes 4 EPS files with logo placement examples. The template can be found here: http://stocklogos.com/sell
You should verify the Transform palette in Illustrator to confirm that your logo is properly centered; the values should be x=1000px and y=1000px while your entire logo is selected.
Bear in mind that the system adds some white space around the final version shown on the website (it also adds our watermark).