CGI::Cookie is what you need, although it's normal to use it through the CGI interface. Cookies are a standard specification. When you read and write cookies, you are using the cookie standard to communicate with the browser.

How the browser stores the cookie is none of your business.

HTTP::Cookies::Microsoft seems to be built to solve a different problem. As I understand, it would be useful if you were writing a Windows web browser in Perl that wanted to read the cookies that were already stored by IE. I don't know why someone would want to that...

However, you seem to be writing a website, so I think CGI::Cookie is the way to go!