Vizit Pro stores annotations in a Document Library called VizitDataStore. This library is located in the root web of the site collection containing the working document. The library is hidden so it must be navigated to directly. Here is a sample URL to the store: http://path/to/root/web/VizitDataStore/
The annotation file name corresponds to the UniqueID (GUID) of the SPFile of the associated working document. The Document Library is locked down to the System Account user, so elevation is required in code to access the annotation document library.
If annotated documents are moved, Vizit does not rename the corresponding annotation file. To work around this limitation, you can create list event receivers using the SharePoint object model to detect this situation and update the annotation file accordingly.