Hi , 

Never taken my bike on a ferry . Has anyone had recent experience of travelling from Newhaven to Dieppe with DFDS Tansmanche Ferrries and what is the procedure for tying the bike on-board . 
Thanks 

Just like anytime you move your bike in a vehicle. They strap it down with tie downs (usually pretty manky) and run it over the bars and across the seat. Your bike MUST be on the centre stand (if you have one) and when I did it I used 2 towels acoss the tank and bars to keep the scratches down. Dont worry over much mate they have done this hundreds of times and definately know more then you when it comes to safe storage. If you can, stay by your bike till they come to tie it down and explain you would like to cover the bike where the straps cross over the bike to protect it, they are mostly good guys who will help if you ask nicely. Good luck on your journey.

i take a piece of carpet, easy enough to stow away as its only around 6" wide and long enough to protect the side panels

You could always take one of those strap thingies that go over your wheel, then they could strap to that...