Unfortunately i use the files very often, so i always would have to use the qkonsole, which could be quite complicated and critical for mistyping.
Note that you don't necessarily need the console; you can use a wrapper script that uses opie-sh to prompt you for the password from Qt and then decrypts the file, starts your app, and prompts you to re-encrypt the file once the app closes.
You would still need to enter the passwords every time you access your file, but there's no way around that if you want to be safe.
I can tell you from experience that a little extra typing is worth knowing that your sensitive data is safe. I had my SL-6000 with *lots* of personal info stolen a year ago and still worry if it will cause me problems.