If your site is using MySql but you want to use MS SQL for the Analytics data, you can do that but you have to run the sql script manually and use a different connection string than the site. This is documented on the System Requirements/Installation tab on the In Site Analytics Pro product page, but let me know if any steps are unclear.
I think the report performance is a little bit better when using MS SQL vs MySql, but I am using MySql on this site both for the site and for In Site Analytics and it works well enough.
Best,
Joe