Here is what I've done so far to handle 3 separate instances upgrading:
<InstanceTransforms Property="Upgrade">
<Instance Id="I01" ProductCode="*" ProductName="Product Instance 1" UpgradeCode="55a25a09-5979-438d-91dd-67755012a288"/>
<Instance Id="I02" ProductCode="*" ProductName="Product Instance 2" UpgradeCode="a27eb2e5-9aa8-4d09-b6c0-df717875c310"/>
<Instance Id="I03" ProductCode="*" ProductName="Product Instance 3" UpgradeCode="d705720d-3703-4b17-817e-bd51edd9abea"/>
</InstanceTransforms>
While my Property Upgrade is a fixed Guid. With this, I can handle 3 instances with their updates separately using this line -for new installs, add MSINEINSTANCE=1- :
msiexec /i MyProduct.msi MSINEWINSTANCE=1 Transforms=":I01"