I just chose Malta as it was a relatively small nation that I knew I wouldn't miss to much in my save game
I changed the teams names in the Maltese league to the ones from the channel islands so I haven't removed any teams. So when it comes to qualifying for Europe and things it all just carry on from where Malta left off.
The national team start in the nations league group where Malta were and the same goes for world cup and euro qualifying
In terms of guernsey and jersey they are created as regions with all the different parishes created as cities in those regions. So I'm not sure how simple it would be in terms of changing that and all the players and staff.
I have been looking at things today and I think I'm going to build a new data base with a separate Guernsey and Jersey based on your Muratti and island games set up. I'll start with that and add leagues, teams, cities, stadiums, media, awards and all the things I had in mine. Will take time but I love doing that sort of thing then being able to play in a fully custom channel islands save 😀