The problem with automatic settings + flash is that the camera sets the exposure for ambient light (ie: without the flash), which, in dim light is useless. In good light you can use exposure compensation to decrease the ambient, and let the flash provide the remaining light.

In manual, it will meter based, and then determine how much flash power it needs to fill in the missing light. The faster the shutter speed, the lower the ISO, the the bigger the aperture f value, the more power it takes. If you make the flash use too much power, it needs time to recharge. There are two solutions to this. One, use a higher ISO. This way, it takes less power to illuminate the scene. But keep it lower enough (or use a high enough shutter speed) that the ambient light doesn't cause issues. Two, use batteries that can spit out power faster. I use Eneloop Black batteries. Alkaline batteries tend to output power just fine at first, but then fade and output less power. Think dim flashlights, etc. That missing power translates to a longer recharge time on the flash. There's even a handy chart.