Hi, laozhang! With new batteries and the original software, your iLiad should act just like it did with the old batteries. Just plug it in and charge it. Your battery icon should eventually fill up. If it doesn't, then something is wrong with your hardware, or else the batteries were already full when you installed them.
If you don't have shell access it will be very hard or impossible to install the new software properly, so you may not be able to get this mod working. You have to request developer access from iRex in order to install my new battery software.
However, the original software should work fine with the new batteries. You just won't see any extra life, because the old software does not know you have new batteries.
Hope this helps!