If you're using fully manual settings in low-light situations, and you want to use autofocus, you can

1: force the flash,
2: depress the shutter button halfway, let the flash flutter help the lens determine the focus and,
3:with your finger still holding the shutter button and locking focus, click the flash down and take a picture.

This way the flash helps you autofocus and the flash doesn't fire, because it never does in manual mode (unless you want it to.)

naturally, in such low-light situations you'll need a tripod and a long exposure time and, ideally, a static subject.