Installing to an “Add-On Domain”

I wish to install wordpress to a second domain name that I have purchased. I have already configured the domain name in my hosting account’s CPanel. I presently run a blog at this same domain provider and it is working well. My dilemma: I wish to have my second/Add-On Domain run in the root directory while its WordPress files reside in a separately named folder. If I do this however, won’t the .htacess/index/wp-config.php files conflict with each other (assuming they are properly configured with the add-on domain’s corresponding information? I just want to think this through before moving ahead but I need to move quickly.