Adding projects to the same invoice is easy to do in Bonsai. When editing an invoice for a client, you will see a link to "Add Project" if you have additional projects with the same client. It should look like this:
Clicking this will open a dropdown to select other projects that you can add to the invoice. When you select it, it will add it to your invoice as a new section where you can add invoice items, add unbilled hours, etc.
That way, when you send it to your client, all of your project billing can be combined into a single invoice for them to pay.