I've got a 12" JL with 300watt alpine amp in the trunk of my accord and I lose a lot of sound through the seat. I have to open the portal door in the seatrest to get decent bass. That's why I was asking about doing two 8" woofers in doors and skip the trunk sub.
From what I've read, a 12" sub in the trunk should be plenty loud throughout the cabin. I don't know if your accord had some sort of special lining between the trunk and the backseat, but the fact that you couldn't hear it very well is strange, the accord is not that big of a car.
My friend has a 12" in the trunk of his civic and it's more than loud enough. I realize the civic is a bit smaller than your accord was, but not enough to make much of a difference. You sure your sub in your accord wasn't broken?