I have installed wordpress in a sub-directory called blg in my root folder. Also, I have served the website from the root following the method given in this codex. My question is, if in future I am planning to create my own website at root and giving a link for blog to the wordpress site in the directory, then my permalink are going to be changed. If this gonna affect my SEO anyhow. Can anyone explain ?
Depending on the authority of your website you will see a massive disruption in your rankings dude to 301's; ultimately the rankings will return to normal in a few weeks. (this of course depends on your distribution of 'link juice'). The new site you are creating will not suffer as you are doing nothing wrong.