A-MSSQL-SKIP-ALTERNATE-KEYS determines whether alternate keys are used to form indexes during table creation. The default value of this variable is "0", which means it's okay to use alternate keys. While the default value is "0", this configuration variable can also take values of "Yes," "No," "True," "False," "Off," or "On."
If you set the variable to a non-zero value (such as 1), alternate keys are not used to form indexes, which speeds up processing if many writes or rewrites are being done. (Note that a value of 1 may slow processing if the application is reading sequentially using an alternate key).
You can load a great deal of data into a table rapidly with this variable set to 1, and then create the missing indexes using ISQL.
See also
The Microsoft SQL Server documentation on ISQL.