I've decided to add a second WordPress blog and I've run into problems regarding the permalinks of the second blog.
Here is my folder structure:
.htaccess (blog 1)
index.php (blog 1)
I've copied the index.php and .htaccess of blog1 into the root to resolve a permalink problem I had with the website. (http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory) The problem is that I would need to do the same thing with the files of blog2, if I want to use pretty permalinks and I've no idea how to do that or if it is even possible to do that.
Edit: Forgot to mention that each blog has it's own top level domain that I want to use. For the sake of this let's call them blog1.com and blog2.com