Glad to hear!
I cannot really tell what is best here. Depending on which FSL template was used, it should even be the same template. mni_hires.nii is exactly the same as the ICBM2009b nonlinear asymmetric t2 template (http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009). Novel versions of FSL at least also use templates from the ICBM2009 series. So anatomy should be quite similar. Depending on the nonlinear co-registration algorithm you would use to co-register the FSL template to the mni_hires.nii template, it could introduce more error than benefit. As said, I just can’t give good advice on this, don’t know any empirical data about inter-template co-registrations.
The routines that visualize anything in lead-dbs are called by ea_write.m -> it’s a simple function from which you can easily find the 2D and 3D calls. If you happen to make adjustments to the functions that could also help others feel free to make a pull request (https://github.com/leaddbs/leaddbs; or just send me the modifications if you’re unfamiliar with git/github).