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This walks through setting up a new server end to end, touching every module once, in an order that makes sense. Each step links to the full reference page if you want more detail than shown here.
1

Invite Petto

Use the invite link, it needs Manage Server at minimum. Petto’s role gets added near the bottom of your role list by default, see step 2.
The Servers without Petto group of the dashboard with Art Club, Petto not added, and an Add Petto button

petto.sbs/dash: a server without Petto has the Add Petto button.

2

Position Petto's role

Open Server Settings → Roles and drag Petto’s role above every role you want it to be able to moderate (mute, kick, ban, manage). A bot can never act on a member whose highest role sits above its own.
liam tries !kick @toxic_tom and Petto answers it cannot kick this member because their highest role is above or equal to its own

In Discord: while Petto's role is below a member's highest role, Petto cannot act on them.

3

Set the prefix, if you want a different one

Default is !. Change it with !prefix <new_prefix> if it clashes with another bot. See Prefix.
liam types !prefix ? and Petto confirms the prefix changed to ?

In Discord: the prefix changed to ?.

4

Turn on core moderation protections

Add yourself and any co-owners to the anti-nuke whitelist before enabling it, see Anti-Nuke.
liam runs the three automod commands and Petto confirms the word filter with warn, anti-raid at 6 joins in 10 seconds with alert, and anti-nuke at 5 actions in 10 seconds

In Discord: the word filter, anti-raid and anti-nuke turned on.

5

Route your logs

Pick a channel (or a few) and send the categories that matter to you there:
Full category list at Logging.
liam adds sanctions and automod to #mod-log and members to #server-log, and Petto confirms each one

In Discord: three log categories, each sent to its channel.

6

Set up onboarding

Add Verification too if you want a captcha gate before new members can talk.
liam sets the welcome and the leave message with --message and Petto confirms both channels and texts

In Discord: the welcome and the leave message, both in #welcome.

7

Turn on leveling, if you want it

See Leveling for the full XP curve and notification options.
liam enables leveling and adds the @Regular reward at level 10, and Petto confirms both

In Discord: leveling on, and @Regular given at level 10.

8

Set up a ticket panel

Full walkthrough at Ticket System Setup.
liam creates panel 1 in #support and adds the support category with the SUPPORT channel category and @Moderators, and Petto confirms both

In Discord: the panel posted in #support, and its first category.

9

Customize how Petto looks in your server

Nickname, avatar, banner, and bio, all from the dashboard’s Customize page, no command for this one.
The Customize page of Petto Land with the preview of Petto, the free nickname field and the Premium profile options

Dashboard → Dashboard → Customize: the preview of Petto in your server and its nickname.

To check your progress at any time, use /setup: it lists what is configured, which permissions Petto is missing and opens a Quick setup form.
The setup panel of Petto Land: prefix, logs, welcome and moderation are done, reports and the setup channel are not, and Petto has every permission

In Discord: the /setup panel of a server that is four steps in.

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What to configure later

Not everything needs to happen on day one. These are easy to add whenever you actually need them:

Automation

Custom commands, autoresponders, reaction roles.

Petto Code Generator

Build commands with buttons, forms and roles without writing code.

Giveaways

Only needed once you’re ready to run one.

Booster Roles

Only relevant once your server has boosters.

Bump Reminder

Only if you actually use Disboard.