Is this the best way? When we upgrade will it delete our hooks or no? If we are doing hooks for a new skin should we just hook the basic skin?
Thanks,
Darren
Using hooks will not be overwritten unless you are adding actual {hook} tags to the tpl files.
Hooks is the preferred method for local customizations. And yes, it is usually best to pick a skin that is closest to the layout and color scheme you ultimately want and then start adjusting (top to bottom usually) from there.