What is the best method to monitor upstream areas for infiltration?  Nighttime isolation and monitoring? 

Nighttime flow isolations can be effective in the extreme upper reaches of the sewer system. However, the most useful nighttime flow isolations are the ones where no flow is observed, as you can automatically rule out these stretches of sewer from further evaluation and not have to worry about the accuracy of the weir measurement. As you go a little further downstream, micro-monitoring then becomes an option, but results from micro-monitoring are perhaps best used in a qualitative rather than a quantitative manner.