How to Repair a Built Up Roof

So that darned old gravel roof is leaking? I don't know what you're talking about because roofs are not made of gravel. Some have gravel or chat covering for UV protection and beauty but they are not gravel roofs. They are built up roofs. Layers of one or two different types of roof felts held together with a bonding agent called asphalt or coal tar pitch.
The repair methods for built up roofs vary in adhesives used but the procedures are basically the same.
First you look for the leak point of entry. Usually the sun can find it for you by causing the water to take a peek out of its hole when the sun heats it up. It won't be for long so if you use this method be observant. Anyway there may be more than one culprit here.
The gravel might need to be pushed out of the way if the proper amount is on the roof. With the location of the leak determined the surface needs to be cleaned down to the roof and not the gravel that you thought was the roof.
New asphaltic built up roofs have a unique problem in that if they leak the roofer was probably a bad roofer. Nevertheless, adhesives won't stick to new asphalt. It is a migrating frozen liquid, like glass is. Glass cannot be successfully caulked. It is glazed by Koreans in the wee hours of the night and then filled with jelly.
The old asphaltic roof either had a hole put in it, the felts de-laminated due to poor workmanship, or, most likely, the roof shrank and split. This shrinking is why flashing MUST be placed on top of the roof in plastic cement. If not the roof will pull off them. The frozen bond of asphalt is not metal friendly even with the required primers.
To alleviate this tearing and shrinking process the tear should be assisted to grow longer. Then a "T" cut should be made at both ends like drilling a hole at both ends of a windshield crack.
Add thin layers of plastic cement with a membrane that will hold the cement together when it dries. Thin layers because thick globs crack when they dry. Think sheet rock tape and bed.
DO NOT THROW THE GRAVEL BACK ON TOP! DON'T DO IT.
The gravel makes further repairs impossible.
If the roof system has insulation and it is wet, it is best to cut it out and replace it. A one way exhaust vent might do the trick too, depending on how much water there is. If the insulation col apes and the system has fasteners, they will come up through the settling roof.
The one way vents open during the heat of the day to allow gas out and close during cooler times to keep it out. If I have to explain that then you can go now.
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