Talk to 10 different divers and you'll probably get 12 different opinions. My advice is to look at various options and understand the "why?" behind them, then make your own choice and try a few different methods in the water.
12/6 versus 3/9 tow cord position?
As you've noted and others have commented there are the 12/6 and 3/9 tow cord position options. Building a bit on what Tom noted, the 12/6 was popular with large lead acid battery scooters. A long 90 pound scooter cruised like a Cadillac with the 12/6 cord position and that still works great in a large passage when making fairly long runs. In contrast, the 3/9 position allows the scooter to be pitched up or down by just pulling on the handle and it makes it much more maneuverable.
However, the sharp downside is that your arm is now part of system transferring thrust from the scooter to the diver. WIth the 12/6 position the cord comes from the 12 o'clock attach point straight back to the D ring, with the lower (and longer) portion of the tow cord then angling down to the 6 o'clock attach point. In that configuration, all the thrust is carried by the tow cord. However, with the 3/9 position, the cord is equal length on each side of the bolt snap and forms a V angling down from the D ring on the diver, to the 3 o'clock and 9 o'clock positions. That means your arm has to pull back on the scooter to keep it level. It's not a great deal of force required, but's there none the less.
Fixed versus floating bolt snap?
Commonly used along with the 12/6 position is the fixed bolt snap. If the bolt snap is fixed on the line you can adjust the distance on each side to adjust the pitch attitude of the scooter. It is again ideal if you want a very stable scooter that basically drives itself. When you combine the 12/6 position with a fixed snap, you can drive even a large DPV with just a finger or two on the handle, and more importantly you can trim it for any annoying tendencies to pitch up or down. That's more important if the scooter doesn't sit in level trim.
Tom mentioned a prusik / slip knot on the tow cord on each side of a fixed bolt snap. Another method is to have a single prusik knot to adjust the length of the tow cord, and then use a larks head knot on the bolt snap to fix the snap in place, but let you fairly easily loosen the knot and move it along the line to adjust the length. Personally, if I am not wearing gloves, the larks head approach is easier, and if I am wearing gloves, it isn't.
The alternative to a fixed bolt snap is a free floating bolt snap where the line just runs freely through the eye of the bolt snap. This isn't as stable, and the scooter can hunt up and down (12/6) in pitch or side to side (3/9) in in yaw as it is not constrained in either direction by the fixed lengths of the towline on each side of the bolt snap. However, this reduced stability also allows for a great deal more maneuverability.
Some hybrid free running bolt snap options.
You can run the tow cord through the eye of the bolt snap 2-3 times to wrap the line around a couple times to increase friction and add some resistance to the other wise free bolt snap sliding along the tow cord.
Alternatively, you can twist the swivel at the base of a free running bolt snap a few revolutions to twist the upper and lower portions of the tow cord together to add friction to retard movement of the bolt snap on the tow line.
Roll then pitch to turn, or yaw to turn?
As noted above with a 12/6 tow cord, and a fixed bolt snap, you could drive a 90 pound Gavin or UV-26 with just a finger or two, once you had everything adjusted properly. As Tom notes, you could make a slow rate turn left or right by pulling or pushing on the cowl with the left hand. That's yawing the scooter to turn.
The other option is to roll the handle to the left or the right to turn left or right. With this approach you roll the scooter in the direction you want to turn and then pull (apply pitch angle) to move the thrust vector in the direction you want to turn. It's a lot more effective when making frequent or sharp turns.
What works best depends on the DPV and on what you are doing.
A 90 pound scooter in open ocean or large cave with mostly straight line cruising is one extreme and at that extreme 12/6 tow cord position, a fixed bolt snap and yawing in the turns works great.
At the other extreme if you have a short, light scooter and you are doing "scooterbatics" then a 3/9 tow cord position, a free floating bolt snap and rolling and pulling into the turns works great.
In between those extremes is where you'll have to make some decisions and some compromises.
For example, I prefer a 12/6 tow cord position with a free floating bolt snap, (especially with a scooter that stays in level trim), as it gives me a reasonable degree of stability in cruise, which I can further increase by putting a wrap or two through the eye of the bolt snap, or by twisting a the swivel a few turns. However, it still allows me to easily roll and then pitch the scooter into the direction of a turn without having to constantly hold pressure on the handle when running straight.
The compromise is that if I pull the scooter really hard into a extended turn, after 360 or so degrees of continuous sharp turn, the bolt snap will migrate so far toward the 12 o'clock position that it becomes dynamically unstable so that the scooter will keep tightening the turn until it ends up against my chest. But I rarely do that, so it's a compromise I can easily live with.
Karst Scuba