Hi Ubendair ..... can I call you Ub for short?
The bottom section of the drain isn't important as to where it's positioned or even how low or high it is in relation to the existing substrate. Of course those decisions will effect the amount of mud used to build your slope .... but not the effectiveness of the shower-pan.
I usually try to keep the bottom section of the drain assembly close to or maybe even setting on the substrate. That means I mix less mud and can have more accomplished in less time.
The top layer of deck-mud requires much more attention. I have several photos linked off the main page of this site which might help.
Try here first:
Shower Pan and liner