I've got a 06 plate Skoda Octavia 2.0l estate L&K with an Audience head unit. The radio's head unit menu shows Aux input but I can't find one anywhere. I've looked in the centre console and the glovebox. What I'm looking for is an input similar to that of my wife's 07 plate Fabia where you can connect via headphone mini jack.

If you lift up the armrest, you will find the AUX in socket.

Mine didn't have an aux port; I bought a cable that you connect at the back to give a (male) aux plug at the front. It works fine although mine might be a different head unit to yours. Worth investigating?

Looked in centre console/armrest,no aux in port in there.

Yes, mine is in the centre armrest on my 56 plate Octy too, on the passenger side if I recall.

The aux port wasn't put in the jumbobox under the centre armrest until the 2007 model year:

http://www.octinfo.com/index.php?p=octavia2_MY_en#MY2007

There will likely be an aux connector on the back of your radio to which you can wire an aux socket as per what SneaksyWhippet said above.

How easy is it to rote an aux connector into the jumbobox? - my 2006 car doesn't have a socket so I'll want to fit one when I upgrade the radio at some point; I'm thinking that putting one through into the glove-box will probably be more straightforward.