I also like using the Paraliminals at night on my IPOD - here is what works for me:
1) Rather then use the timer, just make a playlist (just hold down the track name 'till it flashes twice, then look at the bottom of your playlist menu for 'One the Go' - you can add as many tracks as you want - Alternatively you can create playlists on your iTunes program
2) focus on one thing per night - you might rotate so health tonight, prosperity tomorrow and so on OR you might just decide each night what you need
The reason for this is to let your other-then-conscious mind have time to work on one thing.
3) If you also use Holosync, then listen to the paraliminal, then an hour of floating, then the paraliminal again.
4) If you wake up after the paraliminal, then use just the sleep track only
5) You can also make a recording in your own voice with your 'key' affirmations on it and throw that into the playlist also,
6) I only use the IPOD for 4 hours - I figure my mind needs time to unwind. The exception is if I have insomnia, jet lag and so on.
7) Have fun! I don't think there is really a right or wrong, only what feels good to you - Let yourSELF be your guide,