I spent quite a bit of time searching for an affordable Amsterdam hotel with two separate beds. When I found Hotel Alexander, I was a bit concerned with the size of the rooms, but booked anyway. I don't regret that decision one bit! We did have a small room, but the hotel does an excellent job of packing a lot into a small area. The beds were easily separated, plush, and comfortable, with good bedding and accessible reading lights and power outlets. There was a small refrigerator and desk, with little treats just for us. The shower was really nice.
The hotel itself is really comfortable, with a stylish dining area and reception. They offer luggage storage and 24/7 coffee and water.
We chose not to have a car for the Amsterdam portion of our trip, but we did notice plentiful parking on the street in front of the hotel. I hear it's expensive, though.