Most parts of central Prague have meter zones with fees from 30 CZK to 100 CZK per hour (or you can arrange a long term parking permit). There are some parking lots close to metro stations plus underground car parks. To lower congestion in the city 'Park and Ride' parking-places are used on the outskirts of Prague (at the following metro stations: A-line - station Skalka, B-line - station Zlicin, B-line - station Nové Butovice, B-line - station Palmovka, B-line - station Rajská Zahrada, B-line - station Cerny Most, C-line - station Nádrazí Holesovice ,C-line - station Ládví, C-line - station Opatov). The parking fee here is significantly lower compared to parking in the city,  just 10CZK for as long as you like and the parking lots are guarded.

While parked, however, it's advisable to keep valuables locked away and out of sight of would-be thieves. The roads are in reasonably good condition and petroleum is relatively cheap.

Penalties for wrong parking: 
If you park your car on a place where it is not allowed, very likely you will get a penalty or so called "boot on your vehicle", or it will be completely taken  to the intercepting parking-place. There you will have to pay a penalty and also vehicle‘s towing away fee.
If your car is not on a place where you have left it, inform the Police (158), tell them the number plate of the car and they will find out if your car is in the registration of towed vehicles.