STB will work with any superperms-supporting permissions plugin. The following permission nodes are understood:
For example, to prevent a player (or permission group) breaking Redstone Clocks, add the permission node stb.break.redstoneclock = false to the player or group. The syntax here obviously depends on the permission plugin you're using.
The default permissions allow all actions to be taken on/with every STB item block.
For block protection, larger servers will probably be best served by using a dedicated protection plugin such as WorldGuard but these permissions exist as another protection option for specific STB block and item types.