You can use the command line to create a database snapshot before comparing the schema.
The following xml config creates a snapshot for the database AdventureWorks_DEV and compares AdventureWorks_DEV and AdventureWorks_PROD database in the local SQL Server:
<?xml version="1.0" encoding="utf-8" ?>
<CommandLineParameters xmlns="http://www.xsql.com/sqlschemacmd.xsd">
<LeftDatabase>
<SqlServer>(local)</SqlServer>
<DatabaseName>AdventureWorks_DEV</DatabaseName>
<TrustedConnection>true</TrustedConnection>
<CreateSnapshot>AdventureWorks_DEV.snpx</CreateSnapshot>
</LeftDatabase>
<RightDatabase>
<SqlServer>(local)</SqlServer>
<DatabaseName>AdventureWorks_PROD</DatabaseName>
<TrustedConnection>true</TrustedConnection>
</RightDatabase>
<CommandLineSettings>
<SchemaScriptFile>script.sql</SchemaScriptFile>
<SchemaLogFile>log.txt</SchemaLogFile>
<SchemaWarningsFile>warnings.txt</SchemaWarningsFile>
<ErrorLogName>error.log</ErrorLogName>
<CompareSchema Direction="RightAsLeft" Synchronize="false"></CompareSchema>
</CommandLineSettings>
</CommandLineParameters>
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