Yes, in the case of multiple Magento stores sharing the same stock these Magento websites can have their stock tracked through Megaventory. That feature is possible since Megaventory supports multiple locations out of the box.
All you need to do is to setup each of Magento stores to work with Megaventory as if you would do individually. Other than that there are two key differences.
1. One difference is in the setup of Magento in Megaventory where you need to define the number of Magento installations which will be connected to your account.
There is no limit enforced to the number of installations.
2. The other difference lies in the Setup Wizard in Magento. You will need to choose the value in the Magento Id field which corresponds to the Magento installation in question. Make sure that none of the Magento installations you connect to a given Megaventory account have the same Magento Id set in this field.
Finally, note that each Magento installation can be connected to all or some of the available locations set in Megaventory. This is defined by the Inventory Locations section in the Megaventory Settings in Magento.