Yes, you can still run low chlorine levels, as long as you keep your CYA levels low. Here's the "best guess chart" that we for years have used as a guide to adequate chlorine levels....

http://www.poolforum.com/pf2/showthread.php?t=365

As far as other chemical levels, they're going to stay the same regardless of whether you use bleach, trichlor (the pucks that go in the inline chlorinator), cal-hypo, or any other form of chlorine. The only problem you're going to have is that it's very difficult to keep your CYA level from rising while using a chlorinator, since the pucks that dispense the chlorine also dispense CYA. Your best bet is going to be to use the chlorinator until your CYa gets to 20-30 ppm, then stop using the chlorinator except for vacations or other times the pool is unattended, and just add bleach at night. It's going to be much less expensive in both time and money to go that route than it is to buy the nature 2 cartridges AND the stuff to remove the stains. (By the way, you can also use ascorbic acid to remove the stains--search the forum for posts by mbar, who is the resident expert on stain removal).

Janet