We have a start up company, which we under wrote using $0 for it, but also used an affiliate of the start up company which had over 1MM in gross revenues? Which value trumps which. Page 13 of the CRA guide says for startups put 0. But use the amount of any affiliate you determined credit worthiness with. Which t rumps which?

Was the income of the affiliate considered in the credit decision?

From the Q&A's:

§ 345.42(a)(4)--1: When indicating whether a small business borrower had gross annual revenues of $1 million or less, upon what revenues should an institution rely?
A1. Generally, an institution should rely on the revenues that it considered in making its credit decision. For example, in the case of affiliated businesses, such as a parent corporation and its subsidiary, if the institution considered the revenues of the entity's parent or a subsidiary corporation of the parent as well, then the institution would aggregate the revenues of both corporations to determine whether the revenues are $1 million or less. Alternatively, if the institution considered the revenues of only the entity to which the loan is actually extended, the institution should rely solely upon whether gross annual revenues are above or below $1 million for that entity. However, if the institution considered and relied on revenues or income of a cosigner or guarantor that is not an affiliate of the borrower, such as a sole proprietor, the institution should not adjust the borrower's revenues for reporting purposes.

Yes that comes from page 13 of the guide (3rd column 1/2 way down). Right below it on the same page is the reference:
http://www.ffiec.gov/cra/pdf/cra_guide.pdf

When you use a startup put that revenues are less than 1MM. Both have equal prominance in the guide and both contradict each other.

228.42(a)(4)-3

The difference there would be if the revenue that you relied upon included the revenue of the affiliate you would combine them so you would use the GAR of the start up (0) and the GAR of the affiliate.

If you did not consider the affiliate's GAR then you would only use the GAR of the start up (0).