You can now group textures together to ensure they are outputted to the same atlas. This can be done in the command line using the --group parameter;
gf-pack assets/* --group "assets/ship*" --group "assets/fx*"
Or by providing an array in node.js;
var packer = require("gamefroot-texture-packer");
packer.generate("assets/*", { group: ["assets/ship","assets/fx"] }, function(err){});