Rel canonical for partner sites - product pages only or also homepage and other key pages?

[ArenaFlowers.com]

Hello there

Our main site is www.arenaflowers.com. We also run a number of partner sites (eg: http://flowershop.cancerresearchuk.org/). We've relcanonical'd the  products on the partner site back to the main (arenaflowers.com) site. eg: http://flowershop.cancerresearchuk.org/flowers/tutti_frutti_es_2013 rel canonicals back to: http://www.arenaflowers.com/flowers/tutti_frutti_es_2013).

My question:

Should we also relcanonical the homepage and other key pages on partner sites back to the main arenaflowers website too? The content is similar but not identical. We don't want our partner sites to be outranking the original (as is the case on kw flower delivery for example).

(NB this situation may be complicated by the fact we appear to have an unnatural link penalty on af.com (and when we did an upgrade a while back, the af.com site fell out of the index altogether due to some issues with our move to AWS.)

We're getting professional SEO advice on this but wondered what the Moz community's thoughts were..

Cheers,

Will