I learned using a combo of the two methods. Of the two, I prefer the buddy-cord. I feel it lets you progress faster as the instructor can let you get lower/slower/in more trouble before taking over. I say this because without the buddy cord, there is a 2-3 second lag while the instructor realizes you're in trouble, grabs the box from you, gets his thumbs in postion, gets his eyes back on the airplane and starts to fly it. If you're high enough, it's not a concern... but when learning to land, the instructor may not have enough time to recover.

There are also some students who are reluctant to give up control when they get themselves in trouble...I know of one student who the instructors almost had to wrestle with to take control! For this reason, the instructors were reluctant to fly with this student... you may find your instructors are more comfortable with a buddy box.

Having said this, either method will work. I'd suggest talking to your instructors and getting their opinions on it.. after all, they'll be the ones standing beside you!