Yes, taxis are metered but be certain that the driver starts the meter. They love to charge 20 lira for short rides that would be half or less that by the meter ;)
The last I heard most of Chora Church is closed for renovations. It's also not the easiest place to find when walking as the streets in the area are especially narrow, steep and twisting. St. Stephen's is easy to find however as it's in a park along the shore of the Golden Horn. As someone very recently mentioned in a trip report, while a large section of the Theodosian Walls are very close to Chora Church, it's extremely easy to get lost in that area.
If getting a taxi or asking directions, I very much suggest that you WRITE down the TURKISH name for these sites!!!!! Chora Church is "Kariye Müzesi" or "Kariye Kilisesi". St. Stephens is "Bulgar Kilisesi".