invoicing for a bonus incentive

I was offered a specific bonus amount on top my hourly rate if I could complete a project by a specific deadline. I met the requirements for the bonus. It's time to invoice and I'm wondering if I should include the bonus on the invoice? Is it good business to do such things? If not, how should it be handled?

I should include the bonus on the invoice? Is it good business to do such things

No, it is not "good practice", it is a legal requirement. Invoices are "pay me what you owe me" paperwork, and accounting needs paperwork.

Basically you put the bonus as normal invoice item onto your invoice so everyone who has to know knows what the money is (which includes accountants and tax handlers on both sides of the deal).

You have to be willing to ask. There is an agreement in place, so it shouldn't be a problem or in some way bad etiquette.. Don't rely on someone's memory. If you send them an invoice for a specific amount, that's what the accounts payable people are going to send you.