When it comes to waterproofing the roof, the chimney is generally the most difficult part to deal with. It has to be made waterproof and kept waterproof. This is trickier than it sounds and this is mostly down to the weight of a chimney. Because of this, a masonry chimney will not only settle but also move independently of the property. With the joints between the chimney and the roof broken, water can easily get in and wreak havoc. Due to this, it is often the norm to install two layers of flashing; a base layer underneath and a cap or counter layer on top. Different roofing materials will decide what type of flashing you use. For an asphalt roof, use either roll roofing for chimney flashing or galvanised metal. For a wood or tile roof, use metal. You can use lead for a tile roof if you so prefer and this is a great choice as it quite easily moulds to the shape of the tiles.
You do not have to make your own chimney flashing unless you want to as there are several ready-made options available. Most of these are made of metal and can be bought from roofing supply companies or even from sheet metal shops. The latter one should also be able to fabricate chimney flashings to whatever your specifications are.
If you are using metal chimney flashing, you can choose to install cap flashing over it. Cap flashing is also known as counter flashing to some. The cap flashing is often made of durable metal sheets such as copper and is to be installed in the mortar and bent down over the four chimney flashing cut-outs (one for each side of the chimney). Simply chisel the mortar by a horizontal joint to a depth of about 1 ½ inches, above the flashings. I would use instant mortar for cap flashing and this can be bought from most hardware stores and home improvement stores. Mix the mortar with a little bit of water, making sure to keep the paste thick and well mixed. Wet the area you chiselled and use a trowel to get the mortar into the chiselled area, before pushing the cap flashing into the mortar. Keep it in place for a few minutes until the mortar hardens. I would always wait a day before bending the flashing into place, just to make sure the mortar have set properly.
Flashing and Re-Roofing
If you are roofing over either asphalt or wood shingles, it is important to leave all of the old shingles in place if possible. It is the same thing with chimney flashings. If the existing chimney flashings are in good condition, then you can leave these in place as well. If they look in bad shape, you are better off making new ones and a good tip is to use the existing flashings as patterns for the new ones.