In theory, that shouldn't change just from changing gears. The shift is commanded based on load and rpms, not vehicle speed, so it will still command the shift at the same rpm, which would put you at the same rpms going into 2nd that you were at stock. The reason I say in theory is that it actually will be bumped up slightly, but only because the car will now be faster. There is a delay from when the computer tells the trans to shift, and when it actually does shift. For example, if it wants it to shift at 6K, it might command the shift at 5K because by the time the accumulator fills and the fluid pressure builds, you would then be at 6K on a stock car. Now that you made the car faster, it still takes the same amount of time for the trans to shift, so you might be about 200rpms or so higher when it shifts, which would mean you might be 100rpms higher going into second gear than you were stock. Going the other way, if you take a stock car and do a j-mod to it, you are making the holes for the fluid to flow through larger, and therefor the trans shifts faster. If you don't compensate for this in the tune, the car will actually shift at a lower rpm, even though the computer is commanding it at the same time. What it comes down to is that if you really want to change the shift points, you need at tune, not gears. But gears multiply your torque, so you will probably notice more acceleration from gears without adjusting the shift points than you would from adjusting the shift points without gears. Does that make sense?
