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In the main onboarding flow you can use a wizard to create a github app and inject it using environment variables. In larger orgs there could be a requirement that there are multiple orgs representing department. The github app created is installable on a single org only unless it is published. For enterprise usecases publishing to github marketplace is not feasible. For this reason we introduced multi-tenant github app via connections. Not only does this allow multiple app connections per org but it also makes it fully ui-based and there is no need to set environment variables. The way it works is as follows:

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Prerequisite

As a prerequisite for this step you need to have already set the environment variable for DIGGER_ENCRYPTION_SECRET which is a 32 character string used for encrypting the github values. You can generate one in openssl as follows: The second important point is that you should not have any GITHUB_XXXX environment variables set (example GITHUB_CLIENT_ID) since digger will look for env variables first before it searches for connection matches from DB. 
openssl rand -base64 24

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how to set up multi org connections:

In your backend you can visit /github/connections and it will show you a screen like below