I'm new to Arch. I've administrated many distros before, but never Arch. So I run pacman -Syu to do a full upgrade. Among other things, it updates the filesystem package. So if I don't merge the .pacnew files I can't load from a read-only filesystem. But if I do, Arch refuses to boot, saying that /mmclop505 (not that, but something similar) cannot be found and, entering a panic, loads kdb. What should I do?

It sounds like you are describing several problems here. Can you clarify this, by providing more detains?

It sounds like the first problem is that when you update with pacman, you get a bunch of .pacnew files in /etc. This Arch wiki page explains why this happens. Basically, if you edit a config file, Arch doesn't want to overwrite your changes. So if the package supplies a new configuration file, Arch adds a .pacnew extension to tell you that that's the package maintainer's new default config, and you may want to compare your config to it. (Maybe the config file format is changing?)

For the second part, it sounds like when you try to boot your system, you now get the "/mmclop505" error. Is it saying something like "/dev/mmcblk0p1"? If so, that's usually a built-in memory card reader. Do you have such an entry in your fstab? Try commenting it out or adding "nofail" to the options.

Hope this helps!