If you will be including your EIN on your Schedule C, best practice would be to complete the W9 using your name on line 1, the name of the LLC on line 2 and using the EIN as the identification number. For line 3, you should be sure to mark the box "Individual/sole proprietor or single-member LLC". While there are no guarantees the payer will send the checks in the name of the business, it is most likely that is how you would receive them after filling out the W9 this way. Either way, you will still report the income on your Schedule C.
@RyanCScott
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