I don't know your runtime environment (Spring Guice with injection or
simple Java) but if the latter, you specify which configuration file
you want to load by doing something like this:
Reader reader = Resources.getResourceAsReader("iBatisConfig.xml");
sqlSessionFactory = new SqlSessionFactoryBuilder().build(reader);
You can do this as many times as you'd like within a single program,
so you can load multiple configurations. You then create your mappers
from the desired SqlSessionFactory or SqlSessionManager.
Is this not what you mean?