To implement any design into your store, you will have do something like this:
First, set your main table in "customer/home.tpl" - top cell will include "head.tpl", left cell will include "customer/categories.tpl" and "modules/Manufacturers/menu_manufacturers.tpl"
Second, all the top portion can be set in "head.tpl". Just remove everything from "head.tpl" and put the code for the top portion ("search.tpl" can be inlucded for search area and "customer/menu_cart.tpl" for shopping cart are)
Bottom cell will have "bottom.tpl" included or you can hard code your links right in "home.tpl"
Middle cell will have this one included: "customer/home_main.tpl"
To change your home page, you can change "customer/main/welcome.tpl"
To change how featured producxts section looks : "customer/main/products_t.tpl" (if you want to show products in multiple columns)
"customer/main/products.tpl" (if you want to show products in 1 column)
To change how categories look like : "customer/categories.tpl"
Let us know if you have any questions or want us to implement your custom design for you.