I created a custom template file and I can use it from the "File"->"New..." menu option.
But I was expecting to see it also when creating a new scratch file using "File"->"New Scratch File"
Is this even possible?
(I am using PyCharm 2017.1.2)
I think it's not possible: each time you create a scratch file, it's created from scratch.
Though, what's possible in order to simplify your life, is using Live Templates
: you can create your own abbreviation, which can be expanded automatically to some portion of code. There are many examples in Settings -> Editor -> Live Templates
so you can use them as an example.