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:

• Mee6 (Premium)
• Beemo
• BibleBot
• Birthday Bot
• Chat To Twitch
• Counting
• Dwemer Automaton
• GamesROB
• IdleRPG
• PatchBot
• Tatsu
• YAGPDB

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.)