Auto-upselling products override the standard upselling (related) products. It just picks them sequentially, or randomly from the chosen category or manufacturer.
It's possible to display auto-upselling *and* standard upselling products at the same time, but you'd need to modify /skin/reboot/customer/main/product_tabs.tpl
I've just
tweaked the product modify auto-upselling template, to make it a bit more user friendly, added disable buttons (/skin/reboot/admin/reboot_aup.tpl)