Hi Pete,
When you are send custom emails through your Auctiva account, your current Auctiva store logo should be added to the email in place of the [STORELOGO] tag. I believe the Auctiva logo only shows up in place of this tag when the custom email template is previewed.
If you find that your custom emails do nopt work as I have described, please let us know by filing a support request using the appropriate link on our help page: http://www.auctiva.com/free-auction-software-help/help.aspx
-Mike