#1
I can hear changes in tone depending on where exactly i pick thed string, like between the neck humbucker and single coil, or between the bridge humbucker and single coil.

What i wanted to know is - technically what happens when i pick in that area ? If i select the neck humbucker, do i need to pick the strings closer to the neck humbcuker for a better tone ?
#2
Its just because you're picking the string at a different point. It will change what overtones/harmonics stand out more. Closer to the bridge is a bit thinner and brighter.
Where you pick is up to you, find out where you like it best. You can move around to accent notes too.