I like the concept and convenience of over-the-network upgrades with minimal downtime, but FedUp (Fedora‘s new official method) did not work quite right for my Fedora 18 to Fedora 20 upgrade without some hackery.
Here is what I had to do to get the upgrade to work:
Moved the FedUp cache directories off the /var filesystem (hosted on RAID1 LVM) and into the root filesystem (which required expanding my root filesystem size by reallocating space from elsewhere) and modified FedUp to use the new directories. See Common Fedora 20 Bugs and Bug 1045168 Comment #33 for a workaround.
Added missing LVM kernel parameters to the System Upgrade grub boot section so the upgrade could see the other LVM hosted filesystems. See Common Fedora 20 Bugs and Bug 974000 for more info.
Added missing startup kernel boot parameters to the same System Upgrade grub boot section so it would start the upgrade process instead of booting to a login prompt. See Bug 1038863 for info.
Otherwise I followed the FedUp directions, then after the upgrade completed I tested services and fixed up configs and file permissions that had been changed during the upgrade.
If you are having other problems with a FedUp upgrade, you may want to browse the FedUp bug list to see if any apply and if workarounds have been posted in the comments.
Hope this helps!