Complex Roof Problem
The solution begins with good flashing since this should stop leaks from rainfall and might stop the leaks from ice dams as well. Begin by removing the shingles down to the wood sheathing and slip a strip of adhesive ice-and-water barrier (available where roofing repair products are sold) under the soffit/main roof joint. Depending on how the roofs join, you may have to cut a slot to work it in far enough. It should overlap another piece of ice-and-water barrier laid below, all the way down to the roof edge. This should cover the most leak-prone areas. Then reshingle, sliding metal step flashing behind the fascia board (the trim behind the gutter). The valley flashing, laid over the joint where the two roofs meet, should overlap the step flashing at least 2 in.
If leaks continue to occur from ice dams, consider installing roof edge heating cables. (Find them locally at hardware stores or home centers.) Improved attic insulation and ventilation are usually the best ways to prevent ice dams, but they might not be effective in this complicated leaky roof situation.
Fix Step Flashing
Step flashing is used along walls that intersect the roof. Each short section of flashing channels water over the shingle downhill from it. But if the flashing rusts through, or a piece comes loose, water will run right behind it, and into the house it goes. Rusted flashing needs to be replaced. That means removing shingles, prying siding loose, and then removing and replacing the step flashing. It’s that simple. But occasionally a roofer forgets to nail one in place and it eventually slips down to expose the wall. Check out this article for more on installing your own step flashing.