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There is another way to do that in the zen cart admin. You have to look for it but you can have zen cart left column or not, you can do the same thing for the right column too in the zen cart admin. By setting the zen cart left column to false the zen cart center column and right columns blend pretty much seamlessly with the zoops theme when you actually enter the zen cart area.
It is located under zen cart admin Configuration Layout Settings. Scroll down until you find Column Left Status-Global and Column Right Status-Global. The global setting controls whether or not to have a zen cart left, right or both column(s). This is not the same as the Layout Box Controller.
Sorry for not understanding your problem earlier.
Hope that makes sense? I just hate to see you hack the core code like that unecessarly.
Quest