In R2014b, there is not a way to convert model blocks into subsystems. You could potentially write a script to do this, but it would be fairly complicated.
Additionally, I do not believe you can tune/upload data inside model reference blocks in external mode as of R2014b either.
There is a workaround you could try, however. When you use a model reference, you can define something called "model arguments". Think of these the same as mask parameters for a subsystem. You define a model argument, and then in the reference model you can use that argument as a variable in other blocks (e.g. a Gain block). You can tune the model arguments from the top-level model during an external mode simulation. That way you could still tune some of the values in the model references.
You would still have to create outputs for signals you would like to monitor, however, so you have access to them from the top-level model.
Obviously this is much more limited than just tuning the parameters in the model references, but it does get you closer. Model arguments are explained here:
