Look in the configuration file and set the path in it correctly.
"D:\myproject\MySQL\MySQL Server 5.1\my.ini
Once done, you can set it up as a windows service using the simple command line
"D:\myproject\MySQL\MySQL Server 5.1\bin\mysqld.exe" --install
"D:\myproject\MySQL\MySQL Server 5.1\bin\mysqld.exe" --remove
Change the root password
mysqladmin -u root password NEWPASSWORD
