Can I have an Encrypted Partition in a 2 Partitions USB Stick?
Yes. It's pretty straight forward, to do so just:


Go to Applications / Utilities / Disk Utilities. 
Select the USB device and click Partitions.
Choose the number of partitions you want and resize them as needed.
Choose the format of each partition and click *Apply.
Once mounted on the Finder, Control+Click the Mac OS Extended partition and choose Encrypt.
You'll be prompted  to choose a password. Enter it and click Encrypt Disk.
Wait. Unfortunately, there is no progress bar, so you won't know exactly how long will it take. I just did it with a 4 GB USB drive and it took from 5 to 10 minutes.


And it is done.