Invoice Number Override Add-On
If you'd like to override the invoice number that is generated for a given invoice, you can turn on the Invoice Number Override add-on (Tools -> System -> Add-Ons). When saving an invoice you'll have an option to modify the invoice number by adding a letter for example. You'll also need to turn on the setting Admin -> Billing -> Company Options -> Invoicing & Ordering -> Allow Override of Invoice Number.
You can set up custom order and invoice numbering series on a per-user basis by activating the Per-User Numbering add-on (Corporate level). When editing a user (Admin -> System -> Users) you'll have a new section labeled User Sequences For This Company. You can set the next invoice number for the user along with a prefix and/or postfix for the invoice or order number. The sequences will only be used for orders and invoices created by the individual user.
You can also use the Custom Order Numbering Schemes add-on (Corporate level) by going to Admin -> Orders -> Custom Order Numbering. You can set a prefix for orders numbers and a starting order number. This number series will apply to all users for orders entered in the company.