As I stated in the Infineon guide; the benefit you have being good here is the fact most drivers don't like road courses. At least the majority don't. To like it you need to drive it properly, that way you can make the trip enjoyable instead.
As you can see on the following pictures I marked the path of the car which is more or less the best way around. At this precise lap I managed 1.12.584 (this was way back but the technique is still there).
To get the most optimal time on a qual lap you want to carry as much speed you can coming round for your flying lap. You climb the kerbing placing the whole car outside the supposed track, it's something you always have to bear in mind; use the width of the track as much as you can to maintain speed and momentum.

Now basically, all you have to do is to keep your right foot mounted and shift gears. Approaching the braking zone in 4th gear (sometimes 3rd depending on setup) you brake where the groove in the track starts getting darker. Also, on the left side where you can see the fencing starts changing direction heading off left is a good pointer:

Braking into T1 at Watkins Glen is hard because the track is going downhill and the momentum will push the car forward even more. It's easy locking up the tires, in race conditions it's very important to keep in mind when trying to pass cars, you can play it to your advantage as the opponent might outbrake himself:

You balance the car on the left side of the track as long as you can, shifting down in 1st gear aiming for the apex on the approaching corner:

Here you can see the apex which is the 'peak of the turn' or the very center of it. It's the point you cut in and then fall out again, do not touch the inside kerb as it will only unsettle the car:

Try hit the throttle as early as you can to get good speed out of the corner and therefore gain some time. Practice this and try drifting the car out towards the kerb/extension on the left side as much as you can. I often place my left side wheels on the grass for a moment because it doesn't hurt you accelerating going straight:

Now this is one interesting piece of circuit coming up to the esses. Hitting the rev-limiter in 2nd gear you then hit 3rd gear as you start turning into the corner. As you can see on the picture I have just shifted up to 3rd, placing the car on the very left side of the track, sometimes I place my left side wheels on the grass to gain height into the corner. Watch out though as the grass can make your car drift if you use too much, but usually the uphill climb and the compression makes the car stick so shouldn't be any problems:

In the first corner of the esses you just work the throttle slightly, not using the brake any significant but let the car roll and let the weight slow it down. As the track goes uphill you can experience little more grip as it forces the car down on the ground:

The thing about getting the esses right, is placing the car. Here you can see my speed have decreased just a little, you shouldn't drift the car out to the left side, but stick to the right side of the track as I have marked out with the yellow path:

I still have the car on the right side which is the place to be entering the following left-hander. You want to keep the car in a straight line until you cut in to the left side, it's hard to judge sometimes as you can't see the track ahead, but with some practice this should be no problem. I'm still at the same speed until I start turning left, then I hit the throttle. In qualifying this is all flat-out if you are brave enough and if the setup allows:

This whole section should feel just like one corner, at this point I have committed to the throttle and will not be planning to lift it until the upcoming 'inner loop':

Aim the car close to the left side kerbing without touching it:

Now the track goes fairly level again and you place the car on the right side track close to the kerbing yet again. Shift to 4th and enjoy the beautiful landscape:

Here you enter the famous chicane, aka 'inner loop'. This is a place where loads of loads of time can be gained if you do it properly, you want to hit the brakes somewhere at the "400" sign. If you have placed the left side wheels on the white line it might want to grab the car, so be careful and keep the car in a straight line:

When you pass the "300" sign (which I just did) I start turning in, it sometimes feels too early but the speed of the car will force you to turn early, otherwise you will get a bad line through the chicane itself. You're now down in 2nd gear:

The red marker is where the centre of your car should travel, at this exact spot you doesn't even notice the car jumping or getting any airborne at all. On this lap I was just so slightly off-line as the majority of the car was on the left side of this marker. You should hit it straight on:

By choosing the line into the loop and over the kerb, you will go in a straight line towards the kerbing up front on the left side. You try to hit it pretty aggressive, the car will gain some air, but when it comes down it will generate some grip:

Brake the car down even more, try to keep and force the car to the left side of the track:

Cut the inside kerbing slightly, it is necessary to place the car here if you want a good line into the following long right-hander (called the loop). You wanna be able to maintain the speed:

Now on full throttle in 2nd gear you keep the car straight, as you approach the kerbing on the right side you can cut it but don't cut the grass too much since there is a bump next to the gravel. Small hop won't hurt you:

It's not necessary placing the car all way upside the soft-walls on the left side, but keep the car in the middle of the track. That will give you some height as you cut down the track 'into the corner'. As you notice I'm still in full throttle:

Right here I lift the throttle, at the same time I shift up to 3rd gear. Sounds strange? It's good in race trim as it will be easier on the tires, but in qual I like to stick to 2nd. Make sure you stay low all around this long corner, often many will have a car pushing up the track going off on the grass towards the exit, it's all a matter of adjusting the speed making sure it won't happen. Through the whole corner you like to keep your right side wheels below the concrete path you can see in the track because that will make the car stick. Work the throttle, as I said make sure you stay low:

I'm now in full throttle and at the same time I make small corrections as the rear end of the car will step out a little:

To get the most speed you need to get the car in such a straight line as possible, therefore let the car move over to the left side of the track, use the yellow line in the middle of the track which will provide some grip. Find your limits and use the whole width of the track:

Coming into the last part of the track you place the car on the right side, your braking marker here is where the armco starts bending and closes up the track. Also keep and eye on the racing groove in the track getting darker:

I'm braking as hard as I can without locking up, just some throttle to settle the car, in level with the "200" sign you start turning to left: