How to setup ecommerce tracking in Google Analytics if ecommerce platform is setup on subdomain?

always save the original profile as a backup.

that said, this is an easy problem to solve. you just need to use this line of code above the "trackpageview" line....
_gaq.push(['_setDomainName', 'example.com']);

here's an easy tool to help http://gaconfig.com/one-domain-with-subdomains/

here's more details for your developer https://developers.google.com/analytics/devguides/collection/gajs/gaTrackingSite

Hi, you should use one property with the same UA number on both www and subdomain pages. Enable ecommerce tracking from the profile settings.

Here's the best article on subdomain tracking I've found so far:
http://www.roirevolution.com/blog/2011/01/google_analytics_subdomain_tracking.php

Enable e-commerce for the main profile. If the sub domain is part of the current main site, you should not have to do any cross-domain tracking either.