Linux – Run fsck -y everytime at startup on the main partition Linux

You need to install GRUB to the MBR of both drives, and you need to do it in a way that GRUB considers each disk to be the first disk in the system.

GRUB uses its own enumeration for disks, which is abstracted from what the Linux kernel presents. You can change which device it thinks is the first disk (hd0), by using a "device" line in the grub shell, like so:

device (hd0) /dev/sdb

This tells grub that, for all subsequent commands, treat /dev/sdb as the disk hd0. From here you can complete the installation manually:

device (hd0) /dev/sdb
root (hd0,0)
setup (hd0)

This sets up GRUB on the first partition of the disk it considers to be hd0, which you've just set as /dev/sdb.

I do the same for both /dev/sda and /dev/sdb, just to be sure.

Edited to add: I always found the Gentoo Wiki handy, until I did this often enough to commit it to memory.

You want to boot into your initrd's shell and do the fsck from there, before the root filesystem is mounted. It might involve loading modules in order to get access to your partitions.

This is the reason why having multiple filesystems isn't an unnecessary luxury.