When you write "in uboot", I assume you mean the UBoot prefs program in Workbench.
No, you should not switch to serial, the PATA or IDE, which is what SiI680 gives, is a parallel standard.
E.g. if your "Second Bootsource" used to be "Onboard VIA-IDE Disk", change it to "Parallel SiI IDE Disk", save, then do a full reboot.
You should now be booting from the hard disk connected to the SiI680 card (if otherwise configured correctly).
Best regards,
Niels