When you set a FF profile there is a key called bookmarks. You can set them there:

programs.firefox = {
  enable = true;
  extensions = [
    pkgs.nur.repos.rycee.firefox-addons.vimium
    ...
  ];
  profiles = {
    my-profile = {
      name = "yourname";
      settings = {};
      bookmarks = [
         {
           name = "This is a folder";
           toolbar = true;
           bookmarks = [
             {
               name = "You can nest folders";
               bookmarks = [
                 {
                   name = "This is a lemmy bookmark";
                   keyword = "lemmy";
                   url = "https://lemmy.ml/";
                 }
            ...
        ];
      ];
    };
  };
};

You can always look at the home manager reference, I usually look here.