Hmm...
I can verify the 2.6.6 kernel works fine with raid1, I have it running
on several boxes.
Once you have a system running raid from initrd, std debian kernels
should install fine without the need for modification.
Be sure that you have booted into the raid /root or /boot partitions
when installing the kernel, otherwise the initrd will not automatically
pick-up the modules required at boot time.
You might consider adjusting /etc/mkinitrd/modules to accomplish this
manually, if you are unable to boot into your raid partitions. A CHROOT
into the raid then installing the kernel image will not suffice in
generating the correct initrd.
Zeroing the superblock would be a last resort in my book, but I'm hardly
an expert here.
If you can't boot into the raid, you'll need compile your own initrd
with mkinitrd package and the debian kernel source; modify your
/etc/mkinitrd/modules to have all the appropraite driver modules be they
SCSI, IDE/ATA & RAID => then compile with something like...
make-kpkg --revision=myraid.1.0 --initrd --bzimage kernel_image
Hope this helps,