For Skodas (and VAG in general) OBDeleven is probably the best, as it does coding and adaptations and more detailed VAG specific fault codes. It has a dedicated hardware device. It's pricy, though.
Carista is pretty good too, and also has a dedicated hardware device, and does a lot of the above VAG specific stuff (and specific stuff for other marques too). "Car Scanner" is an iPhone app that I used before I got OBDeleven, and it has similar functionality in that it can do coding. But it's not as widely used OBDeleven, so there's less support for it on the internet. I used it with the Carista dongle, but it should work with any good OBD ii device. Advantage is that unlike Carista and OBDeleven, it's a one time purchase rather than a subscription for the app.
OBDeleven, Carista and Car Scanner will let you configure things on your car like having the rear lights on with your DRLs and loads of other stuff.
If you just want basic OBD fault code reading and clearing, then an app like DashCommand and a bluetooth scanner like this would do. Don't get a WiFi one. Bluetooth is better because you'll still have you phone's internet connection if you connect via Bluetooth, where as if you connect via WiFi, you won't. And if you're diagnosing a fault, you'll want your internet connection.
But I'd personally say that OBDeleven is worth the investment because it's as thorough as you can get on VAG cars without going all out and running VCDS on a laptop..