Here is a basic B&B (if you're looking for something upscale then this is not your place). It's in Prague 6 and the prices are very cheap; includes breakfast. They offer parking. It's run by a family who are very nice. You have a key to the outer door so you can come and go as you please. The reception is not 24 hours but the owners live on prem so you can speak with them if you have any problems. Think Europe from 20 years ago in terms of decor. Very clean.

But...you cannot take a train into Prague. This area is serviced by tram. The tram stops right outside the Pension and is 15 minutes from Old Town and metro or the Charles Bridge. It's in the Castle district, between the airport and Old Town.

I would suggest not staying so far outside town that you have to take a train into Prague. Too much time wasted getting to and from lodging.

Forgot the link:

http://www.penzionchaloupka.cz/

I have done the "train into the city center" approach many times, and I think it is a mistake in Prague, which is a fantastic walking city, besieged by tourist mobs in the daytime but really nice at night and in the morning. It is better if possible to pay a little more for a place within walking distance of the main sites (which are all really close together) or ditch the car upon arrival or pick it up before you leave, if Prague is a starting or ending point of your trip.

Adrienne, the sugggested B&B looks totally fine for us. How did you find the proprietor's english language skills?
We want to keep our car so the secure free parking at Pension Chaloupka is great. Thanks!!!

They speak English quite well.

In the breakfast room there is a refrigerator with beverages and some snacks (chips, candy bars) that you can buy. You take what you want and mark it on the board. Pay when you check out. The owner also sells you tram tickets for your first run into town.

You can buy the tram tickets in the metro station which is the first stop as you cross the bridge. That's also the stop for Old Town Square.

Have fun in Prague and I hope you like the pension.

Looking at the area the pension Adrienne has suggested I would say GO FOR IT. Nice enough area, likely to be quiet at night, tram stop out side and there are even late night trams to the door.The transport system is Prague is really excellent and a 24 hour pass on the trams will only cost 110kc per person.
Prague is a wonderful city and i am back there in 8 days time.

It was very quiet at night - I had my windows open a bit and never heard any noise. It's a residential street in that area so not much traffic going by at night.

unclegus - how many times have you been to Prague? Every time I see your name it's for another Prague trip - you're a great resource!