Martin Krafft did a nice, if overly complicated writeup on disk encryption with Debian.
Martin stated his main motivation for the setup he describes is having separate filesystems whilst still employing encryption, and not entering a passphrase per filesystem at boot.
My laptop is encrypted. I have multiple filesystems, and I only enter one passphrase at boot. I used the standard installer and did nothing beyond what it offered me. I'm using LVM. I have an encrypted root filesystem and an encrypted PV for LVM, and that's the end of my partitioning.