Hi Coby,
Your setup (external usb media at /dev/sdb1 plus SD root) sounds typical. Therefore, if you just enter the following command per the post encrypting-your-root-file-system…, you should have no problems:
curl -G https://s3.amazonaws.com/zk-sw-repo/mk_encr_sd_rfs.sh | sudo bash
The above command will execute using the defaults you have mentioned.