Use the order of operation in the manual, it's right on.
Download the latest control software and update the firmware.
The videos stated are for older versions of 3GX software. Not a big deal, but if you see anything different, just something to note. I run the 5.0. (Not what came originally loaded)
Learn both manual and computer methods of programming. I use a mix of both. Setting the gains is far easier on the computer. Direction of travel, tail travel, and DS settings are easier done manually.
The red ticks on the computer software is a good place to start to get familiarized with flight. It makes the bird docile. I would not attempt inverted flight with these settings. Once used to it, slowly ramp up the travels to insanity if you wish.
My idle up one is 85/80/85, and Idle up 2 is 100/95/100. Awesome.
An item of setup that cannot be overstated is the zeroing of the swash and travels that are set in the DIR (direct mode).
Use a swash leveler and a pitch measurement device to get everything set to zero and equal travel up and down.
If you can turn off the trim switches on your radio, do so. Any trim clicked in will cause problems (Subtrim OK for arm centering).
Lastly, I have found that initializing the 3GX from "as level as you can get" ground, makes the bird more solid. If not absolutely level, I have noticed roll, pitch, or yaw drift in flight. I have landed, unplugged/replugged, and eliminated this annoying drift.