For multilocation quotes always build them by creating the Opportunity from the top-level hierarchy account record.  All location account records at or beneath that level will then be available for quoting.  

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During the quote process, you will have and use only one Opportunity throughout the quoting process even though you may have many locations, multiple Suppliers, and numerous products.

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To add locations oress the "Add Locations to Include in Quotes" button below on the right. If this Account has only a single location it will be shown. If this is a multi-location account, this location and all other locations below this location in the Hierarchy will be available for selection. You may select up to 1000 locations per quote request.

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For information on how to use Account Hierarchies click here.

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You'll see all the Accounts in the hierarchy. In a view something like this:

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Press the Add locations button to add those selected.