How do I migrate multiple store inventories to Shopify?

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I watched the migration video.  Of course, it only shows the drop down menu for locations and shows nothing more.  So,  has anyone with multiple stores migrated?  I am wondering do I migrate each store inventory separately?  Is it as simple as simply migrating the entire inventory that is already separated by store as it is in QB?  HELP!  I do not want to do this more than once.  Better yet, is there an expert that will handle the QB to Shopify migration because the information provided by Shopify is as clear as mud.  

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