I am having issues with the encounters in maps. I have an encounter set up with 6 Cockatrices and my party of 4. If I add all tokens in the map first it will group the cockatrices as one with the same initiative but it will letter them A, B, C...  However I don't want them to all go at the same time so I split the group up but now they are all named the same thing and I can't keep track of them as well. Am I doing something wrong? I did also rename them to "Winged Lizard" so the players don't immediately know what they are as their characters haven't encountered them before. I don't think that matters though because I have done it before and it worked out right i think.

When you add them to the map's encounter it auto-grants initiative and if they have the same name it groups them because that is in line with 2024 rules. This gives you an easy overview. You can, if needed, click icon in the list by the monster group that looks like 2 squares. This will ungroup them, should you want them to have different initiatives.

Here is the view of two enemies being grouped.

If you click Start Encounter, the view changes, with those of the same group being shown separately with A, B, C etc listed after the name. Like so.

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I think your confusion is just that you haven't run the encounter yet.

No, I was running the encounter. I believe the issue was that I changed the name of the monsters from “Cockatrice” to “Winged Lizard” because I didn’t want the players to know what they really were. I ended up having to use the “Cockatrice” name to get the lettering either way, grouped or individual. So they ended up knowing what they were and metagaming the encounter which annoyed me. 

Add tokens to Initiative.

Rename Tokens with the A, B, C added.

Start Encounter.

And there you can have your Winged Lizard A, Winged Lizard B, etc.

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Extra Tip

If this is an enemy they will face often, you can make a copy of the monster ("Cockatrice") and just change the name ("Winged Lizard") and then add the renamed version ("Winged Lizard") to the map. It will then group and auto-add-letters like like any other monster.