FastTrak support was discontinued by both Promise and kernel.org since kernel-2.4.6 (It's not likely to return)
By allowing Fedora to automatically partition your drives, you are in fact allowing it to ignore the FastTrak settings. What you end up with is a normal installation on a single drive, not both. But since the FastTrak bios is enabled, the kernel can't boot a device it doesn't understand.
A raid installation would appear as /dev/ataraid/d0 if using the kernel driver or /dev/sda if using the Promise driver. The fact that you are seeing /dev/hda indicates that only one disk is being used.
If you want to take advantage of the performance of raid, you will need to disable the FastTrak chip (setting it back to the UltraDMA133 setting) and using Linux Software Raid instead. This will however eliminate any chance of dual-booting Linux with Windows on the same array.
I used my onboard FastTrak100 Lite up until FC1, after support was dropped (and after numerous emails to Promise over the last year) I switched permanently back to the UltraDMA100 (I don't use Windows so this wasn't a big issue). I now use Linux Software Raid, which I've found to perform better than the Promise drivers ever did. You should also note that the FastTrak100/133 series of controllers are in fact software raid devices - they rely on the driver (and thus your CPU) to manage the data flow to the disks.