I wonder what people think of this. Document allows catchup contributions. Employer is thinking about simplifying his life by stopping everyone ate $16,500 in 2009. Is it ok to make this kind of administrative decision or should we amend the Document?

Amendment needed. The plan must be operated as written, to the extent consistent with ERISA. Otherwise, a fiduciary violation. ERISA § 404(a)(1)(D).

Can you give me an example of anything that can just be a payroll policy?

Unless your document has a requirement in it, the procedure and the timing for how often deferrals may be changed is normally administrative (meaning it does not have to be in the document).