There are situations where I have had to go in and build a modified version of something rigged in TSM, without access to the original.... You can go in and unhide those geometry bones, turn off the TSM constraints, and still go in and build fan bones, do smartskins, etc...
The best way (IMHO) to smartskins, is to work in an action testing the movement, and switch back and forth between a smartskins relationship--since this isn't intuitive from just saying it, there is a detailed tutorial on my YouTube channel that is worth checking-out...
Since you are rigging from scratch, definately build your fan bones and do the smartskins before you run the rigger.