Quicken will work with your data wherever you store it in general and will remember that location from session to session.
After you have created the container (data vault) with TrueCrypt, with Quicken closed, use Windows Explorer to move the files to the container. Move the complete Quicken folder into the container. The next time you start Quicken, it will not be able to find the last file used (you moved it), so you will need to do a File - > Open Quicken File and browse to the location of the TrueCrypt container. Once Quicken has successfully found and opened the data file, it should find it each time thereafter as long as the container is mounted AND you do it as the same drive letter each time prior to starting Quicken. I'd suggest setting up favorites in TrueCrypt.
Keep in mind, the automatic backups will be created in a Backup subfolder of where the data is stored and that you will want to have your manual backups stored in a different TrueCrypt container that is on different media than where the working copy is kept.
I use TrueCrypt and use the Q drive for the Quicken container holding the working data file just to keep it easy to remember. I also use R for the drive where I do my manual backups to, whether to the network drive or the thumbdrives, that way I always backup to R regardless of where it is pointing to. Just what I have gotten used to doing.