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So I separate my lines based on a main gene. So I have a Mushroom line, Chinchilla line, and Nexus line. I use names to keep them organized. So name would be A# Mu ID NUMBER (# being the generation; Ex: A2 Mu 12345 for a second gen). For Chinchilla its A# Chn ID NUMBER and for Nexus its A# NX ID NUMBER. My stallions get actual names and sometimes I just use the random name generator if I can't think of one.

Now on to who to keep. I cull VERY strictly. I focus very strongly on quality. The majority of my foundation studs are A papered.

1. EVERYTHING gets put through Strict Breeding Advice. I usually do this before looking at any of the foals so I don't fall in love with one that may not pass testing.
2. EVERYTHING that tests Inconsistent gets culled. I do make some exceptions and use a GMT token to make them consistent if they have absolutely every gene I am looking for and they pass the rest of my criteria.
3. Everything MUST test Superior to Sire or Dam. No exceptions. I may hang onto a foal that tests AGA if I intend to boost them.
4. 3rd Gen and up MUST be homozygous for the main gene of the line. So mushroom, chinchilla, and nexus. All 3G+ mushroom breeders must be hom mushroom, etc.
5. I am only just recently trying to figure out a good AFPT culling criteria and it is looking like I need to make it stricter than it currently is.

Basically the best way to go is to pick a gene (or three, like me lol) that you like the most and make that the focus of your line. You can absolutely include other genes in the line but have a main one to focus on. For example, my mushroom line has NO fantasy genes but I have a ton of Satin and DP mixed in. But those aren't the main focus so I only cull on color based around the mushroom. Find a naming method that helps you track the generation and breeding line the horse belongs to. I do also have a 4th line that is basically a gene dump line where I just breed the offspring of my main foundation stud together and breed for quality and as many genes as possible: https://hj2.huntandjump.com/horse.php?horseid=6156020

Also. I used to use a letter of the alphabet to represent a specific gene i wanted to breed for and used it as a suffix in my horses' names. So as an example: So say i made Bb=Chocolate Cc=Chinchilla Pp=Pearl and Ss=Satin. A capital letter stood for Homozygous and a lower case letter meant Heterozygous. Pretend I had a het satin pearl, and hom chocolate 4th gen chinchilla mare. The name would have looked like this: AHH 4G IDNUMBER BCps
I ended up changing my naming system to what I do currently because I realized I wanted a more narrowed focus on specific genes.

If you have any questions please feel free to ask! I hope this helps at least a little!

I am a horse naming fool! I name everything except the horses (mostly new foals) I'm sending to auction. I use tattoos to show generations, and I put a stallions Generation and paper status after their name. I put a z in front of my surrogate mares that are in my show barns, and just use a number to show a gelded stallions generation. That's really it. Sorting by tattoo is the Best Thing Evar!

I have a metric ton of horses and most of the fantasy genes. In order to manage it, all of them go through strict breeding advice first. Then, if I end up with a bunch of studs (inevitable) I look at them all along with ones from the same sire in the previous months and see who I like best. The rest get tossed in the show barn, provided their pt scores are high enough (mine have to be over 10).

At 3g, all of my animals have to be A/Blue. If they aren't, into the show barn. At 5, Star/Gold or the same. I make my 4g studs be Star, but I'll keep the Blue mares at that point. All of my breeders have to have DP on them, regardless, and I am getting to the point where any stud I keep almost has to be hom DP to stay a stud.

As for naming, I generally don't name the show ponies. The mares and studs get named by looking at the names of the others in their lines and smashing things together to see what comes out :)