How can I make each colum box in different colors?
 

In the standard x-cart. There are Categories, bestsellers, manufactureers, special, help navigation..etc in each box with title.

right now all the border, bg colors are control by css.

How can I make each box in different colors?
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You would need to create a copy of menu.tpl for each version, as they all share the same template (menu.tpl) by default.