I'm fairly new to MySQL, but I got it to run properly on my Windows 7 machine. Im developing joomla templates and small php-snippets utilizing MySQL.

My Question concerns the separation of the installation files and the data onto different partitions. I installed and set up MySQL on my C:\ partition and configured MySQL to store the innodb on D:\. On D:\ MySQL creates 1 file called "ibdata1". I was thinking that this was probably a closed data file which MySQL uses during operation.
But every time I recover my Partition C:\ from a backup, I cannot reconnect to my databases. With phpMyAdmin I can see, that all my previous databases are gone even though I did not touch the D:\ibdata1 file. So there must be other files that store information or even whole databases...

Question: Which files do I have to back up in order for MySQL to work properly after a system crash?
And is there a way to store all these files together on a partition different from the installation partition?