That's a decision each runner has to decide for him or herself. Many choose 180 BPM because there is good science to back that pace. These links may be useful for your training:The Simple Way to Injury-Proof Your Stride (for Good!)
Run Tempo plays in the background by default which lets you use it at the same time as other apps that use audio like Run Keeper, Podcasts, etc. You can turn this off in the settings screen.
Yes, the timer works in the background. You can set it and forget it.