In your plugin, you have a lib folder. Create a lib/src sub-folder and move the bulk of your implementation files there. It's typical to be left with just one file in lib e.g. someplugin.dart.
In there you can have any top level classes or functions but this is where you include the implementation source files using the export directive.
Here's an example from the google_sign_in plugin, from google_sign_in.dart:
import 'dart:async';
import 'dart:ui' show hashValues;
import 'package:flutter/services.dart' show MethodChannel;
import 'package:meta/meta.dart' show visibleForTesting;
import 'src/common.dart'; // this import is only required if used by some top level
                          // class lower down this file
export 'src/common.dart'; // this export means that your plugin's users don't need
                          // to import it themselves