there is a query builder on the query tab
http://www.heidisql.com/screenshots.php?which=query
or perhaps you want more of a automated builder like is available in Navicat:
http://www.navicat.com/manual/online_manual/en/navicat/linux_manual/QueryBuilder.html
the upgrade price for eCart will be $99, if you are interested, there will be a live demo of eCart 6 this saturday.