We rented a car and stayed in a small town called Pinto. Pinto is more or less at the border of the Madrid metropole and from there you have easy access by car to PW (about 10 minutes driving) and it's also only a 15 minute drive to PdA.
The hotel was nice and clean, but the surroundings outside were lightly industrial, but you don't notice that while in the hotel. If you decide to rent a car and you are interested in the hotel's name we stayed in, let me know and I'll look it up. Also, if you rent a car, make sure you have a gps with you as the ringways around Madrid are quite easy to get lost in. Or at least make sure you look at the map of Madrid in advance to find out the logic in the ring numbers. Something I should have done before leaving the airport in Madrid.
I don't have any experience with public transport but I know the parks are quite easy to go to by train & bus but then you should look for a hotel near the Atocha railwaystation. You can buy rail-park combi tickets for PW. If I'm not mistaken, you have to take the train to Pinto (yes, after Madrid, Pinto is the place where it all happens ) and take the bus as from there.