Currently I use a labelling system to manage my planets.

I pick a theme for each galaxy. Such as an animal or super hero or whatever.

If there's 5 planets then I simply label them (using Tiger as an example) Tiger1, Tiger2, etc… and I then work the resource flow backwards… i shuttle everything to one planet. I then have that planet sending it's resources to another galaxy etc… until I can have it all sent to a Colony planet.

It just takes so much time managing planets and resource guys and checking up with things… ensuring I label the right ones etc..