Stop articles from a category displaying in main blog category

I have setup two categories as menu items which list all posts in within their catagory and sub categories.

The structure looks like this:
cat1 (home page)
--sub cat1.1
--sub cat 1.2
cat2
--sub cat2.1
--sub cat2.2

Currently if I post in Cat2 or its sub cats they appear in the Cat1 list as well.

How can I stop this happening?

Thanks
Toby