Don't the Lat. pass upgrades come out of J inventory? That shouldn't really change with the eUpgrades as you're not redeeming any certs for them.

And what do you mean by complimentary upgrades? Like Op-Up or the complimentary pass upgrade? If Op-Up, then I think if you're upgrading using eUpgrades, it's very much possible, as is the case now, that AC will gobble up your eUpgrade before Op-Uping you.