I spent a fair amount of time working on my Discord Server to make it secure, functional, and fun.
Here's a general guide to how I have mine setup.
Hopefully you'll find something in here beneficial for your own setup.

Bots in Use and their enabled functions:

• Mee6 (Premium)
  1. Welcome and Goodbye Messages
  2. Custom Commands
  3. Reaction Roles
  4. Audit Logging
  5. Channel Content Restrictions
  6. Searching
  7. Voice Recording
  8. Timed Messages
  9. Statistics Channels
  10. Temporary Voice Channels
  11. Stream/Social Media Alerts
  12. Levels (silent)
• Beemo
  1. Bot Raid Protection
• BibleBot
  1. Bible Verses
• Birthday Bot
  1. Cross Server Birthday Notifications
• Chat To Twitch
  1. Discord/Twitch Crosschat (not quite stable yet)
• Counting
  1. Counting Game
• Dwemer Automaton
  1. ESO Notifications
• GamesROB
  1. Social Games (haven't played with it much yet)
• IdleRPG
  1. RPG
• PatchBot
  1. Free Game Notifications
  2. Game Update Notifications
• Tatsu
  1. Levels
  2. Pets
  3. Housing
  4. Fishing
  5. Other similar stuff I haven't messed with.
• YAGPDB
  1. Automod
  2. Logging

Basic Security Setup:

1. Remove all permissions from Everyone role. (I also explicitly deny Everyone the View Channel permission on every channel)
   
2. Create a basic role with appropriate default permissions. (I also explicitly set the role's permission on every channel, but that's probably overkill)
   
3. Add the basic role permissions to the appropriate public channels.
   
4. Setup a Rules channel and give Everyone role View Channel and View Message History access.
   
5. Setup a Rules message with a reaction role to accept the rules and get the basic permissions role. (I use Mee6 bot to setup my reaction roles since I'm using it for a bunch of things.)