From what I have seen on the web, this seems to be a regular question, without an answer. In Outlook, you can specify where and when the signature appears in an email, but not so using web based GMail or Google Apps. Having it appear at the bottom of an email you have replied to seems quite silly.
Finally I have found the answer, thanks to this link and enable the Signature Tweaks lab. Its a shame that you need to use a third party lab app rather than this functionality built into GMail.
To enable, go into GMail, click on the settings cog, click on Labs and do a search for Signature tweaks. Now when you send a new email or reply to an existing email, the signature appears under your reply/message.
After using Google Apps for several months now, I can safely say there is no going back to the “old days”..well done Google
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