Hello there,
The behavior you both described is occurring because our system doesn't really allow you to *edit* the default winning bidder email template, even though the options on the interface suggest that you can do so. We hope to address this deficiency with a future site update but I'm uncertain when that may happen at this time.
In order to set up a new default winning bidder email template from your existing default one, you just have to give the template a different name after making the desired changes and it will be saved as a new one.
Once you have done so, you can then mouse over the Sales tab and select the Manage option next to Custom Emails to set the new one as your default. Once you are on that page, you should be able to set the desired winning bidder email template as the default so it is used for automatic emails.
I hope this helps.
-Mike