The Space Ship Under the Apple Tree.
Edit: A few story elements that I remember from when I read the books 30+ years ago:
- In the first book, the spaceship is a UFO-shaped ship that is hidden under an apple tree but otherwise obviously a spaceship.
- In the second book, the spaceship is disguised as a car, but with an invisible shield around it. The family's chickens enjoyed sitting on the invisible shield, the protagonist speculates that it lets them feel like they're flying.
- The protagonist (Marty? Or was that the name he gave to the "Martian"? I don't remember) suggests going to get something at the general store. The alien refuses, not wanting to interact with General Store of the human military.
- In one of the later books, the boys return to the alien's home planet. In the dense spacelanes near that planet, the ships all carry a strong electrical charge, so that they repel each other and are thus unable to get into accidents.
- The smaller ship that comes down to Earth docks with a larger ship in orbit to take the boys back to the homeworld.