Deploying jt400.jar or jt400Native.jar in same Websphere application

Hello,
I have a Websphere application that utilizes the toolbox classes. For 
development we use an intel server running Websphere accessing an application 
on the iseries and also another test environment running Websphere in iseries 
partition. Deploying the application to the intel platform we need to use 
jt400.jar and on the iseries we need to use jt400Native.jar. We can have 
jt400.jar as a utility jar in the Enterprise application and referencing 
pojects have a Java JAR dependency on that jar, however that's not what we want 
for deployments to the iseries. How can we seperate out the jt400 jars so we 
have a common source base but can deploy to different platforms?
 
Any suggestions would be very welcome.
 
Thanks,
Mike