Yes, do it all in the main scene - it's the only scene you have anyway (in the "Dodge the Creeps" tutorial, that is). You only need to retrieve the score from the file once - when you launch, so do that in _ready()
.
From then on, you have it in a variable, highscore
for example. Set the label's value with
$SomeLabel.text = "High Score: " + str(highscore)
When the game ends, do something like
if score > highscore:
highscore = score
# write value to save file