I stopped charging batteries in the scanner when a cheap set I bought a Micro Center shorted out and started melting in the radio, thanks goodness I caught them before the scanner was damaged it just melted the battery holder. I had a set do the same thing in a charger also. Don't buy Ultra brand batteries from Micro Center.
If you charge the batteries in the scanner you may not be fully charging the batteries. I bought a energizer charger that came with 2400mh batteries but I could only get about 6 hours on a charge. The charger indicated that the batteries were fully charged in about 6-8 hours and I would get 6-8 hours out of them.
I recently purchased a La Crosse BC700 charger that I am very happy with. It has a LCD that shows voltage, hours on charge, milliamps of charge added, and lets you select the type of charge, test mode, refresh, discharge. When it finishes charging it goes into trickle charge mode but you should not let your batteries set in the charger for a long period of time. It comes with a owners manual that explains alot about charging batteries.Takes some time to learn how to use it, but I just let it default to a 200ma per hour charge rate, takes about 12-13 hours to charge a 2400-2500mh battery. I seem to get about 10 hours with the back light on low, volume on about 15 scanning analog motorola system. I use energizer 2400mh, radio shack 2400mh, and sanyo 2400 mh. The best batteries are the sanyo but are more expensive, I am not sure the extra cost equals the performance though. I get about the same run time with the energizer and radio shack, maybe about an hour more with the sanyos.
I change the batteries when the scanner shuts off, I have the sounds/ beeps set to stealth so the low battery warning does not sound. The battery gauge does not do a very good job I agree. Mine too will operate for 2-3 hours when the battery indicater is very low.