Dear Marco,
Thank you for your question!
You can do this in the Editor. You can a new section in your invoice.twig where the invoice.MerchantReference can be added.
If you are unsure where to do this, please get in touch with our support team and we can have a look at your file in detail.
We look forward to hearing from you: info@wallee.com
Sincerely,
Dewi