Originally Posted by gLk*zaP 
The way you did it IamATeaf works of course. This guide is meant for people who have installed Windows on a drive connected to a ICH8/9 port, not for other controllers. Because then you cant just enable it in the BIOS and install the driver, Windows wont boot.
It should work this way too, you just need to move the drives over to the Jmicron first, let the system boot up so that any config changes are made, then shutdown, change the ICH8R to AHCI, boot up and install the drivers, then shutdown and move the drives back onto the ICH8R. This is infact what I did the very first time I installed the OS on my system.