I would like to know if all Presets irespective of what type they are, should be stored it the Preset>Tool folder in Photoshop CS.
Also can I use subfolders of the Tools folder to store them.
If you want Photoshop to be aware of them when you launch the program, then yes, they should be in the presets folder. You can always load presets from another directory once you're within the program.
As for using sub-folders, I'm not sure, but I suspect Photoshop will read them.