I don't think this has been answered in a way which will be easy for you to understand, so I will have a go.
On a 6 string guitar, it will be impossible to play any 7 individual notes at the same time, you are right.
However, to play an E major
chord, you
do not need to play all 7 of the notes in the E major scale. Instead, you simply play the most important notes of the E major scale.
Think of an E major chord as it like a 'E major' curry. A curry has many ingredients (a major scale has 7 notes), but you only need three basic spices (three notes, E, B and G#) to get the essential flavour of the curry (the sound of E major).
Most chords only use a fraction of the the notes used in their corresponding scale, and will often include an individual note played on two or more strings at the same time. For example, when you are playing an open E major chord, you are playing the note E three times, on three different strings. However, it the sound is 'flavoured' since you are also playing the other important notes of the E major scale (B and G#).
I hope that helps, it really isn't worth getting bogged down in the ins and outs of music at first. I remember my own bafflement when I was told you can play the same chord in different possitions on the guitar
I know, but it really isn't necessary to go into such detail when explaining it to a begginner.