Injury Prevention

Hi everyone, I recently got new shoes and not sure if they just aren’t doing me well. I’m pretty flat footed and I run long distances usually. I keep getting blisters on my feet and went to Fit2Run to get some insoles so I didn’t need to get new shoes. However, my old blisters with insoles keep chaffing against each other so my blisters got even larger. Is there anyway to prevent this?