In practice

'How do you put SV Method into practice? Do you think of a different scale on each chord, for example?'

I put this method into practice in improvisation. For me, improvisation is when you make up something on the spot. That could also be adding extra notes in an existing piece.

Besides that, I also use this method to translate the melodie in my head to my instrument. Because a melody consists of a set of intervals and I can see these intervals on the neck, in whatever key, it makes it easier for me to directly play what's on my mind.

I think of a scale on each chord. I do so for various reasons. The first reason is that, in this way, you always see the intervals relative to the root note (of the chord played at that moment). That makes you conscious of the sound an interval gives in a chord. Then you can choose to play - or don't play - the interval(s) that are characteristic of the scale.
The second reason is that it easier to play over exceptions. When you see an exceptions, you change the intervals of the associated scale relative to the chord. When you always think of the relative scale, you only have to think of the changes you have to make.

In the video below I show how I use the scales while playing. 

The chord progression I used is exercise 7 of chapter 4.3. The progression in the video is played a half step lower.

The first thing you can see, at 0.21, is how the sticker changes by root note
You see that I adjust my fingerings to the finger I play the root note with. From 0.31 you can see that I play the scale of Bb with my middle finger, the scale of Db with my index finger, the scale of F with my pinky and the scale of Eb with my middle finger.
While playing, I always think ahead of the next root note. At 0.350.400.42 and 044 you can see that I play towards the next root note.
I also use the sticker to play across the whole neck. I do this by seeing the root note at different places across the neck. You can see an example at 0.47.
Besides that, I can choose to play another chord-tone other than the root note as first note of the bar, as can bee seen on at 0.54 and 0.59.
I can also play chords, as I show at 1.02.

By using this method in my playing I create much freedom, overview and insight for myself. Besides that, I have stimulated myself to get used to the sound other scales give because by analysing exceptions I could put these scales into practice. When I eventually got used to the sound I naturally started to use these scales in my playing and therefore gained a lot of possibilities and because of that, got new inspiration. 

What I would like to mention is that improvisation does not only consist of melody, but also rhythm. That's a part that is not (yet) been dealt with in this method. As I said before, this method is intended to help you to find beautiful notes, but when and where you play them is up to you.