To visualized the superimposed structures on JMol you have two options:
Load 2 structures to JMol and perform RMSD calculation for your structures and provide the results. I heard RMSD calculation is possible using JMol, but I have not yet tried this option. You could take a look at the JMol scripting options for more information about the RMSD calculation using JMol.
Use an external program (there are many programs available, you can write on your own using BioJava or for an example you could look at a python implementation here)to calculate the RMSD and load the superposed structures to your JMol window.
I think the second option is more feasible, as I am afraid the performance of JMol depends upon the JVM settings and it may not be a good idea to superimpose structures at the client-side.