Give each company its own branding
Make sure each company's invoices and receipts show its own name and logo.
Switch into the company
Use the company switcher to enter the company you want to brand.
Set its branding
Go to Get Paid → Settings and add that company's logo and colours.
It follows the document
Each invoice or receipt automatically shows the branding of the company that issued it — not whichever company you're viewing from.