Q:

Archive structure and effects on SEO

With a wordpress setup as follows of pages, custom posts, a custom taxonomy of colours and rewrite rules in place:

Pages:

Archive:
-fruits

Single:
--fruit/apple
--fruit/orange

Archive by colour:
---fruits/colour/%colour%

-vegetables
--vegetable/potatoe
--vegetable/carrot
---vegetables/colour/%colour%

-colours
--colour/red
--colour/green

etc ...

I could quite feasibly structure archives to be found at the following

fruits/colour/red
or

colour/red/fruits
In the context of how a user could navigate a site I can see the benefits of having both paths available but pointing to what is essentially the same content. 
Should this be avoided with respect to SEO and avoiding duplicate content?  

A:

If you need these two URLs being accessible for users, you need to choose one URL as the indexed one for search engines and put to the second one a rel="canonical" tag refering the first one.  That way, these two URLs will be accessible for users but just one will be marked as valid (= indexed) for search engines to avoid duplicate content issues. 
For example, you choose the first one (http://www.example.com/fruits/colour/red) and in the second one, you add this tag <link rel="canonical" href="http://www.example.com/fruits/colour/red" />.  That way, all the SEO value will be associated to the first URL.