I moved Atom from my SSD (where the OS is installed) to a mounted partition I use for everything else.
The following will assume your new partition/drive is already mounted at startup in /etc/fstab
as /storage
(It can be anything, but that's the hierarchy I used.)
What this does:
Before beginning, exit Atom.
Prepare the "home" directories on your second drive:
mkdir /storage/atom &&
mv ~/.atom /storage/atom/.atom &&
ln -s /storage/atom/.atom/ ~/.atom
Now the "config":
mkdir -p /storage/atom/.config &&
mv ~/.config/Atom /storage/atom/.config/Atom &&
ln -s /storage/atom/.config/Atom ~/.config/Atom
Prepare the elevated directories:
mkdir -p /storage/atom/usr/share &&
mv /usr/share/atom /storage/atom/usr/share/atom &&
ln -s /storage/atom/usr/share/atom /usr/share/atom