We used AutoTrader to find our EOS. AutoTrader has a very good search options box where you list your 'desired' options. However, it also tells you how many cars are listed for sale with those or other options and you can play around with your choices.
You are searching for a used EOS in a limited and diminishing market. From those search results you can get an idea what the most popular options are. Using color as an example, we found black EOS's the most common, but there were only 6 at the time in Leoni blue/beige that we wanted. We traveled half way across the country for our 2007. Do the same for automatic DSG and manual transmissions. You will find more manual options available.
Unless you have a lot of information on a used EOS history from a private seller, consider paying more from a genuine VW Dealership, but watch their extended warranty because it may not include roof leak problems.
Your features wish list seems a bit strange. We got a Tdi (manual) 'Sport version' and later I wished I had a highline version with inclusive features like cruise, HID lights and radio steering controls. These are VERY expensive to fit retrospectively. When buying older used cars that have dropped a lot in price, consider the high end feature versions as you will get better value.
Knowing what I know now about potential DPF issues, I should probably have chosen a more feature rich 2 liter petrol EOS in the same color. But our Tdi in this heavy car returns 51 mpg touring mpg and 45 around town. The Sport Tdi also has less electronic complexity and looks nice.