We generally set the top of the rocker with the top of the frame. This will hide the frame rails as Craig mentioned and usually yields a 4.5"-5" rocker ride hight. But with that comes other issues like Craig mentioned. It introduces issues such as front sheet metal mounting, radiator support modifications (remember you're now lowering the way the entire body fits the frame), the trans tunnel become larger than normal (due to the trans being pushed up in the floor) then that leads to throttle pedal clearance issues etc.
That is why its a good idea and sit and or talk to a shop about HOW and WHAT you are looking for. Anyone can throw a number at you. But that number may be the simplist method and may not be what you invisoned.
One modification usually leads to another and this is what makes estimates on custom work difficult. A good builder works with the knowledge of whats next down the line or what will result from the current modification. A bad builder does what you ask and after hes paid can care less of the finished product after it leaves his shop. Like others mentioned, you're looking at close to 250 hrs. Those two shops that estimated 5-6k are a little off IMO.
I'm just trying to prepare you... dont want to see another member get shafted.