For communal hosted customers with QuoteWerks, their SedonaMaster Company table should use the named instance (e.g. SQLAWS1\ExampleSQL) in the ComputerName and Document_Server columns. See below example. LoudSec_Final is linked to QuoteWerks and uses the named instance in the appropriate columns instead of the SQL alias: 
The QuoteWerks DB setup should also use the named instance: 
The technical explanation is that the QuoteWerks integration buttons (though not the QuoteWerks DB Setup menu seen immediately above) use named pipes to connect to SQL with a query joining the QuoteWerks database (connection pulled from the QuoteWerks DB Setup menu seen immediately above) and the SedonaOffice company database (connection pulled from SedonaMaster Company table seen further above using the old standard method without the newer named instance columns and the QuoteWerks integration was never updated to use said named instance columns).
Lastly, you will need to make sure that the customer’s TSPlus server is added to linked servers on their named instance by running
sp_addlinkedserver CustomerTSPServerName
Where CustomerTSPServerName is the name of their TSPlus server. The initial query to get the database connections appears to pull the QW DB Setup from the Company DB and then pull from the SedonaMaster Company table, so it needs their TSPlus server as a linked server in SQL on the named instance to do so.
