Welcome to Nikonians. I believe it would be very important for you to study the manual and make certain that the custom settings are set in the manner that you desire. Regarding the focus, the a1 & a2 (custom settings) will play a part in that along with how the lens is set (A or M) plus the auto focus mode button (AF or M) on the camera body.
To really get the most out of your camera I'd suggest getting a good book, such as Thom Hogan's Nikon D7000 guide or D. Young's book. Nikon's manual is good but really leaves a lot to be desired, imo. I have Thom's ebook along with his "go to" guide and they go into great detail plus suggestions on different custom settings. The more you "play" with your camera and lens the more you'll learn and since digital let's you see the results immediately you have nothing to lose. Good luck.
Nobody should seek his own good, but the good of others. <><