nikon - How can I improve my exposure in low-light situations?

I am new to photography and have been struggling with low light scenarios. I have a Nikon D3100 and an SB-900 flash. Regardless of my ISO, aperture, or shutter speed settings, when I am photographing inside a church (common setting for me as we hold scouting events there), my pictures are just not as exposed and briliant as I want them to be.

I just purchased the Nikon 35mm f/1.8 lens hoping this will help with indoor low light shots. I like to do portrait shots as well.

Any suggestions on settings I should use? Should I use it indoors in low light with my SB-900 flash, point the flash angled toward the ceiling? Bump up ISO to 200-400?

Attached are a couple pictures from inside the church I usually shoot at for our Eagle Scout ceremonies...