I recently installed Ubuntu with an encrypted home folder. I now have a second drive that I want to use to store my pictures, music, etc. I was thinking of creating a partition on the second drive for each folder on the home directory that I want to use it for (e.g., one partition to mount to ~/Pictures, etc) and then mounting each partition to its corresponding folder. If I do that will the information stored in the folders on the second physical drive be encrypted by virtue of being mounted under the home directory? If not, can I run Ecryptfs on the new partitions so that the encryption works the same as for the home partition (i.e., decrypts at login, etc)? Also, is the best way to accomplish what I'm trying to do?
If you're setting up new partitions on the new drive, you'd might as well use encrypted partitions with cryptsetup / LUKS.
eCryptfs and EncFS are for encrypting some folders on a filesystem, LUKS is for encrypting an entire partition. See archwiki for a good overview of different disk encryption systems.
With the new partition(s) encrypted, then you can use any type of link or just a shortcut to the new encrypted partitions, and any data anywhere on the new partitions will be encrypted. You could even have the new partitions automatically mounted when you login (storing the keys in your encrytped home) or mounted at boot, or on-demand.
Don't worry about mixing linked encrypted files and only relying on eCryptfs to carry the encryption to a different drive (which probably won't be encrypted if you only link the decrypted folders anyway) it just sounds like a data leak waiting to happen.