When you first sign up for Monarch there is a dashboard card called "Getting started" which will walk you through the 4 steps (in order) on how to best get started with Monarch.
Generally we recommend you connect as many accounts as you can before you start categorizing transactions, setting up rules or budgets. If you have a lot of accounts, start with your main banking and credit card accounts where you have the most frequent transactions. It's easier to add investment accounts, real estate or loans later since they aren't as impacted by the initial set up steps.
The most important part of the flow is to not skip ahead to "create a plan" until you have most of your accounts and categories setup since Monarch will analyze and give recommendations based on the average of your last 3 months of spending for your plan. If you are missing accounts or don't have the categories configured the way you prefer the 3-month analysis may look wrong.
Here is a good order of help articles to follow along with each step: