For those wondering how to get it to work in For: Science! (0.2.x), please read this comment.
DISCLAIMER: Usage of deprecated mods is not advised for the long-term. Keep an eye on your CKAN
FINAL NOTE: This works as of 19 Dec 2023, KSP2 0.2.0.0.30291 --- If you see that UITK, BepInEx, SpaceWarp and Custom Flags are all becoming compatible, you are heavily recommended to uninstall the mods detailed down below. (And to then switch to the compatible versions)
1 - Get CKAN for KSP2 (https://www.youtube.com/watch?v=b7cDexZq_zY)
2 - CKAN will start with "is:compatible", click the X in the search bar to disable this filter.
3 - Browse for "UITK For KSP2". Click it. Press Versions. Then select the most recent one available.
4 - Browse for "BepInEx". Click it. Press Versions. Then select the most recent one available.
5 - Browse for "SpaceWarp". Click it. Press Versions. Then select the most recent one available.
6 - Browse for "Custom Flags". Click it. Press Versions. Then select the most recent one available.
7 - Hit "Apply". You will get a warning that these are outdated. Tell CKAN that it's all right.
8 - Now in your KSP2 folder, create a "flags" folder. Insert your .png file(s) here. Make sure they are at least 512x300px.
9 - Through CKAN or Steam, launch the game. You may need to launch it twice if this is the first time ur launching with these mods.
10 - Enjoy your custom flags