Hello,
You can encrypt APFS volumes (and partitions that formatted as Mac OS Extended (Journaled)) by mounting the volume or partition, then going to the Finder. Right-click (or hold down Control as you click) on the volume or partition, then choose Encrypt. You'll be prompted to create a password that will be used to encrypt the volume or partition. Be warned that once you start the encryption (or decryption) process, it cannot be stopped.
About APFS:
When you format a partition as APFS, what happens is that the newly-formatted partition is transformed into an APFS container with a single APFS volume inside. An APFS container, like a partition, is rigid in size; it cannot automatically resize itself as it needs. However, the APFS volumes inside the container can resize themselves as they need. The total amount of space consumed by the volumes in an APFS container cannot exceed the size of the container itself. Most MacBooks are formatted as a single APFS container (partition) that takes up the entire space of the SSD. Inside this container, macOS High Sierra creates four volumes that it uses:
Preboot: Used to store FileVault unlock information and login windows for all startup disks in the container.
Macintosh HD: Your startup disk. This volume may be named differently.
Recovery: Contains Recovery Mode for all startup disks in the container.
VM: Used to store sleep image files.
When you created a second area on your SSD for your sensitive data, there's two ways you could have done this. You could have created a new APFS volume that would be added to your currently existing container, or you could have literally partitioned your SSD so that two APFS containers exist: one with your startup disk in it and one containing the volume with sensitive files in it. I recommend simply creating a new APFS volume within the already-existing container, since APFS encryption applies to individual volumes and not to entire containers. (Even if you create a new APFS container and format it as Encrypted, that will only apply to the first volume in the container.) In addition, the sensitive data volume could grow and shrink as it needs along with your startup volume, allowing (almost) the entire space of your SSD to be available to either volume.
Hope this helps!