Is it possible to make the PCB I want to do?

In short, I want to make a PCB of an atypical shape without starting out with individual parts first in the EDA software, I want to draw and run the traces without having parts placed first. Is this possible, and which software would be best? I’m willing to spend money on the software.

I’m sorry for the lame and ambiguous title, I don’t know how else to title this. I’ve had the hobby of electronics for years, but I have never delved into making my own PCBs. I’m just now getting my feet wet, as in my little toe is in the water.

The Knowledge I have so far on EDA cad programs so far suggests that what I’m trying to do could be particularly challenging if it’s possible. I could be wrong. I’ve been working on and off on a project for a long time and I’ve hit a road block of fitting all the components and things into the shell(An original style DMG Game Boy Shell). I haven’t worked on it in probably close to a year. The solution I’ve come up with is to to make a PCB that all the individual systems such as a Raspberry Pi, soldered on the bottom side of the PCB to the GPIO pins, a ProMicro Arduino, and an adafruit 1000c power supply soldered to the top via IO pins, along with a few other miscellaneous components. It’s essentially just a way to eliminate all the wires, and the piece of plexiglass I have everything glued to pictured here. The PCB would just be a way to connect all the off the shelf systems to a board that would basically turn them into a single Raspberry Pi shield with a wonky shape.

First, from what I understand, with most EDA software, there’s generally an order of operations that is followed to get from idea to a Gerber file to send to a PCB house. This includes, having dependencies in the EDA software for all individual components and placing them down, then defining all the connections to produce a schematic with “rats nest” connections. This is almost like a breadboard representation of the circuits. After that you run the actual traces and come up with the digital representation of the PCB and make sure everything works on paper so to speak.

What i face is I’m not just placing individual components like resistors and capacitors, but entire systems such as the a small Arduino and a power supply that’s connected by IO pins. This will essentially be a sandwich of stuff. Is there software that has these things in a library that I can select these things as components themselves to place down to run their connections as if the whole Arduino and power supply for example were like regular ICs in a manner of speaking? The dimensions, spacing, and IO pin alignment will be extremely important.

The second constraint is defining the shape. It will have to be exact to fit in this shell and not just a regular rectangle. I know this is likely possible, I’ve seen plenty of PCBs that aren’t just a rectangle, but my question is, which software would be best suited for rendering an atypical PCB shape?

There has to be two 8mm Holes for the screw posts to pass through it. The upper right corner will have to be cut out to make a space for the small cooling fan I got. There will have to be a square cut out of the center for the heat sink of the Raspberry Pi underneath to protrude through. There will be sections of PCB, 11mm X 10mm protruding from the two bottom corners for the back buttons to solder to.

If all else fails, I assume I could design the overall rectangle size but with silk screen lines that define areas I could cut out all the sections with a dremel and make sure all the traces are within these cut line boundaries to get the final shape. I was thinking that might be best anyways for the first version prototype so that I could use that to gather data to get the final dimensions.

Is this a pipe dream, or is there a particular EDA program that would be more suited then others to achieve this idea?