I'm sure there's specific epoxies that would claim to work but I'd find it hard to trust them, especially with the likelihood of putting something into the trunk that bumps it.

Do you have the amp mounted so that the fins are vertical or horizontal? Vertical would allow the heat to rise up over the fins a little bit better - in IASCA competitions (once anyways) the judges would look for that actually.

Are you feeling brave? Are looks important? Have you considered taking the case cover off of it? It's almost assured to be using the case itself as a large heatsink, but you may find a spot in the middle that isn't touching anyhting. Perhaps cut a large hole into that and nount a fan right over it? Something like a computer case fan in reverse. Of course you'd need somewhere else for the air to blow out of.

Anyway that you do it, I think that the closer the fan is to the amp the better, but you can't sit it face down on it or the hot air will have nowhere to go. Blowing down onto it, about an inch or two away...

Generally the cooling fans I've seen used involve the amps being in a plexiglass case of sorts, or an MDF (Medium density fiberboard) case with a glass or plexiglass cover. Then the fans are mounted to one side of the case, with open air holes on the other side for the hot air to escape through. If you've got it on the back of a seat, that might not be too bad actually. The box may look nice (paint it or carpet it), and also ensure that the air is doing it's job in the area that you want it to be.