Yeah the best way is to create nandroids of each rom slot to your ext sdcard.
After they're made delete all the rom slots you created within TWRP itself (boot options select each slot and then select delete for each) afterwards boot into your stock rom slot.
On reboot open the SS app and choose uninstall recovery. Then open your phones main "Settings" and select Apps.
Scroll down to SS and delete it's data&cache, click force stop and then uninstall it.
After that you're all good but I personally use Root Explorer to find my backups in the TWRP/BackUp/XXXXXX/ folder & move all of them to a different folder on my ext sdcard for safe keeping.
Once that's done I proceed to delete the SS & TWRP folders on my sdcard & ext sdcard.
Once you install the new version, open the app & install it's recovery. Then reboot into it and create a new stock nandroid. Then select Advanced from the main menu then File Manager and use it to move your old nandroids to the newly created TWRP/BACKUP/#s/ so you can then restore your rom slots.
I only posted this so those of you who are a little anal about your phone (like I am) you'll have a more complete way to format and reinstall the new SS.
Sent from my DROID BIONIC using Xparent ICS Tapatalk 2
Pretty much what I was thinking the procedure would be. Think I'll just stick with what's been working with 3.5 since I have a few projects that I'm working with on 2 slots plus my DD until I absolutely have no choice. Thanks for the clarification!