An upgrade is when a completely new version of the software is released. The release will have a new version number. For example, if the current version is Amicus 2012 then Amicus 2013 is an upgrade.
An update is an interim release or patch to an existing software program. Updates are sometimes referred to as service releases. They are released to add small new features, fix known issues in the software and/or to ensure compatibility with 3rd party products and operating systems when required. They are small releases and are identified with number extensions within the same version number. For example, if the current version is Amicus 2012 then Amicus 2012.1 is an update. Updates are only provided to currently shipping Amicus products.