I've been briefly looking into downside of having two links to the same place in a web page, and it doesn't seem to me like there's anything that wrong with it. I don't think it impacts on SET at all. The only thing I found was this - saying it can muddle up your analytics a bit but that's not the biggest problem: http://www.savio.no/blogg/a/102/how-to-track-multiple-links-to-the-same-url-automatically-in-google-analytics

However, I do think having a navigation at the top to take you to a different site can be confusing because people could get it confused with the main site nav.

You'll notice your situation is very similar to Stack Overflow who have loads of sites and put them all in the footer (scroll down). You could do that. I also like the way Mozilla do it, with the pull-down "Mozilla" button at the top (effectively putting the "footer" at the top of the page).

I don't know if there is a definite best practice for this, just decide which you think is neatest and go with it.

I've been briefly looking into downside of having two links to the same place in a web page, and it doesn't seem to me like there's anything that wrong with it. I don't think it impacts on Search-Engine Optimisation (SEO) at all. The only thing I found was this - saying it can muddle up your analytics a bit but that's not the biggest problem: http://www.savio.no/blogg/a/102/how-to-track-multiple-links-to-the-same-url-automatically-in-google-analytics

However, I do think having a navigation at the top to take you to a different site can be confusing because people could get it confused with the main site nav.

You'll notice your situation is very similar to Stack Overflow who have loads of sites and put them all in the footer (scroll down). You could do that. I also like the way Mozilla do it, with the pull-down "Mozilla" button at the top (effectively putting the "footer" at the top of the page).

I don't know if there is a definite best practice for this, just decide which you think is neatest and go with it.