I just can tell you that you do not need two design folders if you use two siteaccesses.I usually have one site access for each language but all of them use the same design folder.
If you want to have two different root folders you have to have two siteaccesses anyway, otherwise your user will see the same startpage for each trademark. Still I think sections might be useful to tell which content belongs to which trademark. Of course you could always add a selectbox to each class for trademark1, trademark2 or both.
