Unless you are into car racing, I think your should consider Automatic. Especially if you need to drive during rush hours. It's so comfortable to drive (and play with your mobile while driving - not recommended thought!). A complete peace of mind.
I have used CNG with Civic Oriel 2005 Automatic for 3 years. I would say it was just OK (and great fuel costs savings - at least 10,000 rupees a month). I have now sold this to someone (thru PakWheels) who was not happy with CNG performance. He got it checked and realised that the CNG fitting didn't have advancer and emulator (or whatever they call it). This I guess is something new and wasn't there when I got by Civic CNG'ed.
He installed the advancer and emulator and now he is so happy. He called me to tell that he has taken the car to Murree and Pir Sohawa and he didn't even feel that the car is on CNG.
Alhamdulillah I have just received my new Civic 2008 Automatic and I am considering installing CNG once the 1000km running is over.
So my suggestion would be - Go for Automatic. Manual is thing of past now!