Our billing system is similar to yours in that we have numerous sets of rates.
At the moment - We bill off-site
SEO (linkbuilding, etc.) at the admin rate as it's not technical. On-site
SEO is a natural part of the design/redesign process so ends up getting billed at the programming and design rate. Consultation is billed at the admin rate as well.
Hope that helps! What are your own inclinations with this issue?