I wonder if it is a good idea to add my sites to my Google Webmaster Tools account? I'm asking especially because I have my sites linked between each other and when Google sees all these sites added into one webmaster tools account, this may harm my sites, can't it?
You can add both of your sites into Google webmaster Tool because you just need meta code to implement it into your website.
Why not? There is no harm in linking your websites to each other as long as their business is related to each other and these sites are beneficial to the user... And we can manage many websites under one Google webmaster account... So, do not worry much about it.