Yeah, it should charge both batteries fine. I've done it both ways.
Even after the battery indicator goes off it is still trickle charging so I still leave them hooked up for a while after if you are worried about squeezing every last ounce of juice out of the batteries. Think the way lithium ion batteries work is it charges rather fast up to about 90%, then the last 10% takes a while longer to do.
Here is a post I saw when I 'googled' the issue a while ago:
"4 hours should be more than sufficient to fully charge the battery. If the
player is off, the battery icon will go away in about an hour (probably
less), and the charging circuit will go into a trickle charge mode to
charge the up the remaining 10% or so. It shouldn't take more than 4
hours, so allowing 4 hours should be more than adequate. Besides a new
battery will come to you about half full (40% or so)
--
Harvey Fong
Technical Marketing Specialist
Audio - Speakers - Portable Digital Entertainment
Creative Labs Inc. - USA
http://us.creative.com"