Usually the preferred side is decided by the railway owner. In France most trains always remain on the port track, however some neighbouring countries and even some specific areas of France do it the other way. In order to prevent any risk of collisions between opposite trains, the interface between these areas swap the sides with a bridge, so that opposite high speed tracks never cross each other.
Regarding stations, most high speed rail lines use platforms on both sides and on a separate track. The main high speed line tracks remain together at the centre of the station, and the extra tracks separate on each side so that trains can still run on the high speed line at full speed even while an other train is stopped at the station. There is usually a small wall between the main tracks and the station tracks to prevent people from crossing on foot. I think this design is ideal as it allows to build the track without stations and then add the station later on top of the track with minimal track modifications. (at least in your 3D software)
You can try to find some architectural inspiration from current on-the-line high speed train stations "built in the middle of nowhere". Their design is usually very compact. The thing which takes the most space is the car park area, bus stops and the highway access.
Here is for example Aix en provence TGV station with quite good looking architecture. (the station sits between the arms of a highway)
For building such a station in an urban area, you can stack the elements on top of each other with a carpark either underground or on the roof (or both), the station ticket office, and services area at ground level and the tracks above.
Or do it the other way around like at Valence TGV station, with the track down in a trench and the station built over the tracks.
Here are the smaller and simple Lorraine and Champagne-Ardenne TGV twin stations (no protection wall, just extra space between the tracks)