Let's put it this way. I am looking for M/T:)
Sir PROSMATEC are much better then manual because they are trouble free in both driving and CNG, that is why they are most sought after and expensive then their M/T counterparts.
M/T's clutch/suspensions are often messed up as they are driven hard.
However, you can also look for a M/T Civic, if you like.
How do I check the Car Electronic System (Computer) is working properly ?
Sir you cannot check it yourself at the time of buying, unless you take the cars to Honda 3S or any qualified technician to diagnose ECU code or error, if any.
IDSI engine is the most tricky thing in the car, look for performance and condition (oil leaks/spark plugs/coils) thoroughly on both CNG and Petrol.
After that comes the suspensions and body, look for rust/dent/paint closely.