First of all, I have been in this hobby now for, oh, 10 years or so and I have at least two planes with NiCd packs that are still working just fine. A routine cycle seems to do the trick. So, so much for alaursen condemnation. I will say, though, that I do have and use NiMH packs also. There are some differences, but for the average hobbyist, well, they are not worth mentioning. Use what you have. If they work, and if they are stable (note my first post about using packs and if you trust them or not). As I said, it depends on if they have been sitting around and if they will hold a charge after a cycle.
Now to answer your question, tomcatguy, again, I am not familiar with your charger, but if your particular charger has cycle capability, then it should be able to tell you where to stop, or stop automatically and go right into re-charge. Cycle... run down to minimum then cycle back to, or change to, charge, automatically.
But, again, battery packs are not expensive. If you feel you don't trust your battery pack, I would recommend you replace it with a new pack. There is a lot of information available on batteries, battery packs, charging, cycling, and so on. Check out this web site:
www.radicalrc.com and read what you can in their FAQ sections. Lots of good information from a professional.
CGr.