Let's say your mount point for the TrueCrypt container is named ~/EncryptedFolder. You would do the following:
1. Unlock the TrueCrypto container and mount it to ~/EncryptedFolder
2. Copy your existing wallets to ~/EncryptedFolder
3. Tell ArmoryQt to start from that folder:
python ArmoryQt.py --datadir=~/EncryptedFolder
All wallets you create/add in that instance of Armory will be saved in that folder. If you don't want to copy your existing wallets manually, you can restore them from their respective backups from within Armory as well.
NOTE: if you do this on an online machine, the db data will end up in your encrypted folder, unless you give it a specific path with --dbdir. If you want to encrypt your public keys on your online machine, that's an ok thing to do.