To get access to the data on your stick and to copy files onto it you need to mount the eCryptfs. This involves several steps:
First you should insert your stick. If Ubuntu doesn't mount it automatically (It usually does.), you should mount it.
Now you should find a directory called .Private. If you did a default installation, this directory should sit in /media/DISK/home/.ecryptfs/USERNAME/.Private. In this example DISK is the directory where your stick is mounted and USERNAME is the name of the user you entered at installation. If you can't find it yourself open a terminal and enter
sudo find /media -type d -name .Private
I assume in the following steps that the directory is in /media/DISK/home/.ecryptfs/USERNAME/.Private.
You need the mount password. This is different from your login pasword. Enter the following command into a terminal:
ecryptfs-unwrap-passphrase /media/DISK/home/.ecryptfs/USERNAME/.Private
You have to enter the login password from the installation of your USB-Ubuntu (not your usual password). The command outputs a passphrase. Write this down or copy it into a file.
The password enables you to unlock the directory. You need to do it in two steps:
> ecryptfs-add-passphrase --fnek
Inserted auth tok with sig [123456789abcdef0] into the user session keyring
> sudo mount -t ecryptfs /media/DISK/home/.ecryptfs/USERNAME/.Private /media/myUSB
The first command adds your passphrase to the kernel keyring and the second tries to mount your .Private to the directory /media/myUSB. If the latte doesn't exist, you have to create it first:
sudo mkdir /media/myUSB
The mount command will ask again for the passphrase. Please enter the output of the above command. Next it will ask for a cipher and key size. You should accept the default values (aes and 16). Type n for plaintext passthrough and y for filename encryption. The last thing is the FileName Encryption Key (FNEK). Look at the output of ecryptfs-add-passphrase --fnek. There are two lines starting with Inserted auth tok …. Insert the value in square brackets of the second output (123456789abcdef0).
Now you can access the files in /media/myUSB and can copy from and to the directory or subdirectories.
A large part of my description is from "Live CD method of opening a encrypted home directory".