I don't think there's a problem of having navigation bars or menus placed right or left up or down. You'll usually find them to the sides of the screen.
- Blogs have menus usually on the right side, and horizontal navigation on top.
- Regular web pages, have menus on the left side, and horizontal navigation on top.
But there's no rule about having navigation anywhere on the site, as long as it easily accessible and consitent you wouldn't have any problem.
I've seen a couple of websites having two horizontal menus (like UX.stackexchange.com).
I think that the valuable thing to keep in mind is to keep things organized.
Consider having multiple horizontal navigations, one could be your meta-site links, and the other your actual links to products or services.
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Just make sure that Home is the first element of the list.