Loading x86 or x64 assembly

There is built-in support for this in 1.0.80.0 and later.

If the development and customer machines may have different processor architectures, more than one binary package may be required. For this situation, using the native library pre-loading feature is highly recommended. It is available as of version 1.0.80.0 and enabled by default. (from download page)

However, to get it to work in my own plug-in I also had to add this before referencing SQLite for the first time:

// Make SQLite work... (loading dll from e.g. x64/SQLite.Interop.dll)
System.Environment.SetEnvironmentVariable("PreLoadSQLite_BaseDirectory", System.IO.Path.GetDirectoryName(System.Reflection.Assembly.GetExecutingAssembly().Location));

Sql.Data.SQLite...

See this question: New SQLite mixed assemblies

1. install appropriate DLL in the GAC (e.g. 64bit version on a 64bit platform)
2. use assembly binding in your web/app configuration (possibly in machine config)
3. Fully qualify any partial assembly references in your web/app config.