Hi,
my email is sam.eden@sky.com
I have my products setup like that but i am not using the shortcode to output on the homepage as i have my shop page setup differently,
My products output like this
(main/top) Alternators
(sub)BMW
(product) M3 Alternator
(product) etc.
(sub)Mercedes
(sub) -etc.
(main/top) Starter Motors
(sub) BMW
(sub) Mercedes
(product) C Class AMG Starter
(product) etc.
That is how i have mine setup, and only the top level displays, then the sub category etc etc.
But i only access mine through the shop page.