Learn about your boot-loader, Grub or Lilo in most cases. The bootloader can boot multiple operating systems and multiple kernels.
The key to never getting stuck with a bad kernel build or other problems is to never overwrite the working boot record with a new untested one! Instead, build the new kernel, add a new boot record for it, and if it fails simply boot back into the working kernel.
Exactly how you set up the boot-loader will likely depend on your distro as well.
And as answered by others, the filesystem is usually irrelevant as long as it is a GNU/Linux filesystem to start with.
Last edited by astrogeek; 02-15-2014 at 10:38 PM.