Kernel advice for 13.04

So I just installed Ubuntu 13.04 on my Toshiba laptop yesterday. I've used Linux before but not for a while. As soon as my install was done I got a notification for some updates, including a kernel update. I installed but afterwards my computer would not boot. I got an error saying "kernel panic not syncing vfs unable to mount root fs on unknown block" and after that all I got was the GRUB command line.

I looked up troubleshooting steps for this online but I could not get any of them to work. I booted from a live CD and tried to mount the system from it but it kept saying the mount points didn't exist, then I got more problems with chroot. I am guessing this is because I set that install up in an encrypted LVM.

Anyway, after trying and failing to make it work, I just did a clean install (with only my home folder encrypted, no LVM this time) since my initial install was only a day old anyway, and now I have it back up and running (and dual booting with Debian perfectly).

My question, however, is now I have it up and running, how do I update the kernel on Ubuntu without the same problem coming back? If I don't let the built in updater do it, but instead update to the latest Linux kernel manually with a tutorial like this, will that avoid the issue?

Thanks in advance.