Assuming that the church is like most churches i.e. rather dark inside, the flash will be your main (only) illumination.
Use your flashmeter to read the light reaching your subject from the flashgun (this could be averaged from the middle and edge of the group, as suggested) - this is the aperture to set on the lens.
Take an ambient light reading from the same spot - this is for your shutter speed, using the aperture previously established. How much slower the shutter speed is compared to your lowest comfortable setting will, in general, be how underexposed the surroundings outside of the flash pool of light will be. Unless you light the background seperately with additional lights or balance the ambient with the flash, the background/surrounds will always be darker than the main subject.
Tricky area but hope all goes well.