The Aux input cable is terminated in a set of RCA jacks. You'll need a cable that goes from RCA plugs to a standard headphone plug - these are readily available at any electronics store.
Then, you have two options. First, you could plug the headphone plug into the headphone port on your iPod (duh). Change the volume on your iPod, and the volume through your Elise's stereo changes too. Not the best situation, as this can lead to distortion if too loud, or, if the iPod is set too quiet, and you switch to FM, you be shocked by a blasting stereo.
A second option for connectin the iPod to the headphone jack is via the iPod's lineout connection. To use this connection, you need an adapter. I use the imp. It has the iPod dock connector on one end, and a y-cable going to a lineout connection, and a connection going to a cigarette lighter plug for charging the iPod on the road.
I like it a lot because just one wire runs to the iPod and the aux. out is in the cig. lighter plug part. It also has a level control. I also have the remote for my iPod, which I find indispensable for using it in the car (no looking, just grab the remote and click through tracks). It won't work well in the Elise though because of the location of the outlet. It's perfect in my Jetta. Really good in my Miata. Not so good for my Audi (but not terrible). I'm thinking about getting an Icelink for the Audi. I hadn't worked out a plan for the Elise yet (there's lots of time for me, sadly).
The location of the charger throws a wrinkler for recharging the ipod, however, we're looking at nearly 8-10 hrs of life which is more than adequate for any road trip. I for one am not about to leave my ipod on the charger, talk about a tasty bait for theft. So it'll come inside with me anyway where it'll reside on a charger.
I highly recommend learning how to use playlists (piece of cake) they come in very very very handy on a roadtrip.
Just got my IPod on Friday. It's a 20GB w/ dock, holder and remote from apple for $249. Yes, it's the "non click wheel" model but from a "while driving" view, it's probably better than the newer models. Trying to get up to speed quickly with it since my car is due any day (or so I'm told).
In my Miata I have an Ipod in the trunk. There is a 12 volt adapter running it and I have taken the remote headphone cord and extended it by soldering about 10 feet of wire. The remote is in the center armrest. I just keep it on random and flip through the songs I do not feel like. I plan on doing the same on the Elise. The adapter turns off when the car turns off. If I forget to put the Ipod on pause then the worst that will happen is the ipods battery runs down not the cars.