While it may SEEM like a good idea, most vape shops recommend that you do not charge the batteries inside the mod. The USB port is mainly for upgrading your mod's firmware. From what I've been told, it's mostly because if something decides to go wrong during charging, say if you have low quality, damaged, or faulty batteries, they might vent, taking the mod with it. If that does happen, not only do you have to replace your batteries, you also have to replace your mod at this point. I'd say that's a pretty strong reason to avoid charging your batteries inside your mod.
Now there are exceptions. Some mods have the batteries built into the mod. These you CAN charge through the USB port because that's what they're designed to do.