When you select charge, but not balance charge, you are "bulk charging" But the charger will slow the charge dramaticly at the end of the charge for safety, making it a lot safer than using some kind of bare bones power supply.
If you select charge, not balance charge, and connect the jst plug you still get single cell monitoring while you charge, but not balancing. This can be handy, for spotting a problem cell that charges too fast because it's capacity is low.
Well, acutally, 50w is already pretty dramaticly slow.
Then you half it.
It will work fine, and safely. Particularly if you are trying to extend battery lifespan by selecting lilo charge, and only charging to 4.1v.
THE LIPO RULES. NEVER ABOVE 4.3V NEVER BELOW 2.7V DON'T PUNCTURE
Ideal charging /discharging range for Lipo, 3.65v minimum 4.1v maximum
See battery technology section, FAQ thread at the top of the page for lipo noob info.