They appear in the middle of the system? For me it was the bottom-right corner of the map lol.

But yeah, you have to convert the ship's .mesh file to text format and add a hangar hardpoint anywhere on the model (coordinates 0-0-0 work, and noone ever actually looks at the SC so you can stick to those until you have nothing else to learn/improve)

Then, in your ship.entity file, you need to change the "maxNumCommandPoints" to your desired squad limit, and specify (up to 4) squad.entity files for the ship to use. squadTypeEntityDef: 0 through 3 set these .entity files, and the corresponding squadAntiMatterCost: specifies the AM required to build the SC (Capships generally build SC for free)