Use something like this.
Pick a dry day. Not too hot though!
Rough the mineral felt with a steel brush so it cleans it, removes dirt and loose dust and stones, for the area that the flashing will cover plus an extra 3" (this is green mineral felt I presume). Then brush it clean.
Drill the hole in the correct place and brush away loose dirt/dust/wood.
Prime the area to be covered (including the extra 3"), with Firestone RubberCover quick prime plus.
Put the pipe through the roof enough to get the flashing over it. Think about soldering distances from rubber, think about Gas pipes passing through voids etc. I know you will have but thought I would say it anyway.
Once the primer is tacky, seal around the pipe and roof with Stixall black adhesive.
Run a couple of circles of the same adhesive around the pipe hole (on the flat roof) approx an inch away from the pipe and again an inch in from the edge of where the flashing will sit.
Cut the flashing so it fits tight over the pipe (which is clean and grease free). Push it down nice and square onto the roof and press the base down well.
Prime the top edge of the flashing over 2" - 3".
Cut and stick down 'Form Flash' rubber in a neat square over the top so it overlaps onto the roof by 2" - 3" and similar onto the flashing and press it down well. That can be done in four strips or, two with a semi-circle cut out of each or one piece with a circle out, obviously this is dependent on size.
Run a nice neat bead of the black Stixall adhesive around both edges of the 'Form Flash' and the exit point of the pipe. Put the tip of the Stixall 'just inside' the rubber as you go around so it gets between the pipe and rubber.
You can use deck flashings with metal bases but with those we always screw them down and make sure the screws are sealed with Stixall beneath the head and on top before they are covered with the Form flash.
Beware, Form flash will stick as soon as it touches the primer, especially in hot weather. It is expensive stuff and great care should be taken to align things correctly before it goes down. You cannot always get it off without destroying it.
Better with two pair of hands.
The above method is the one we use mainly for flue pipes. It as never leaked and we are happy with it. I have not seen the roof you are working on but it sounds like this method will work. My advice is to go and speak to a roofing/plastics centre near you for more advice on materials which are suitable for the roof you're on. They may offer a different suggestion. They are normally very knowledgeable (for obvious reasons) and helpful.
Hope this helps.
