1) what set of results/files do you want to transfer to the template? In general, you would need to perform a registration between the subject files and template files. If you have already processed your T1 data with SVReg (and BrainSuite extraction) then results can be transferred to the BrainSuite template. If you want to transfer to ICBM then you would need to perform an affine registration with register_files_affine tool (or any other tool of your choice).
2) Visualization can be done in Brainsuite itself.
3) mergeDWIs and register_files_affine are matlab functions and has to be used from through matlab. Details and examples of these functions are available at http://neuroimage.usc.edu/neuro/Resources/BDPAddons