To have a name that is different from your company file name printed on your invoices, first download an invoice template from under the "Template" section of your company settings.
Highlight the row of the table that contains the Company Name. Delete the entire contents of the row.
Edit the company name, save, and upload it under in the template section of your company settings.
Once you create the invoice, click save and close. Then from the invoice you created, click the Print icon and choose the template you created it. You can then save your invoice (with alternate company name) and either email it to your client or print it out.