As a general partnership, you will indeed be filing a separate partnership tax return (form 1065) in addition to your personal tax return (form 1040). The partnership will issue both partners a Schedule K-1 which will be used when preparing your personal tax return.
If the services provided were done through the partnership, then you complete the W-9 based on the partnership information.
*A reminder that posts in a forum such as this do not constitute tax advice.
Also keep in mind the date of replies, as tax law changes.
