The problem of choosing where to pull stock from for your online Shopify Store has a simple solution.
You can create the Inventory Locations you would like to pull stock from only in Shopify.
If, for example, you would like to pull stock from your locations in the US and the UK only, then you should only create these locations in Shopify -with the exact same name as in Megaventory- and do not create other locations.
At the same time, you can create more locations (eg one in Germany and France) in Megaventory and hold additional stock there - but this will not be shown in Shopify as available.
You can make this additional stock available to Shopify by doing an internal transfer from France to the US, for example.
Or login to your account!