Alright then, what you want to do is spud (scrap surface to remove the stone aggregate) from around the area you will be installing the flue stack, probably a 3’ x 3’ area. Be careful not to damage the roofing felts while spudding, and I recommend you spud the roof while it is cool outside and before the sun heats up the roof. If you gouge the roof membrane, you will have to spud out a little further so you can patch the roof. Next you need to cut the hole in the roof. You want to make sure you have the right spot, so I would suggest you drive a long screw driver up through the bottom of the roof deck until it pokes through the roof membrane (actually, do this before you spud so you know where the center of the flue stack will be located). After you have spudded the roof, mark on the roof the circle that is representative of the flue stack so you know where to cut. Next, get some 2x4 and picture frame the circle but stay back approximate an inch from the circle. Mark the inside and outside perimeters of the 2x4’s and cut a square in the roof to match the inside dimension. FWIW, the 2x4’s should all be the same length, don’t go the two long and two small piece route. To cut the square, use a utility knife to cut the felt, and whatever works to cut the insulation/lightweight-concrete or whatever is there. If it is iso board or something along those lines, a drywall saw works great. Let me drop back and say the outside edge of the wood nailer you are preparing to install should be about 1-inch wider give-or-take a little than the flange of the base flashing, because you are going to set the flange on on top of the wood nailer. Cut the roofing membrane diagonally from inside corner of hole you cut, to what would be the outside corner of the wood nailer. Fold back the roof membrane without breaking the felts if you can, and now you cut the insulation even with the outside edge of the picture-framed wood nailer. Once the roof is cut and the insulation is removed, you want to cut the hole in your metal roof deck for the flue stack. You can use a saws-all, or if you know how a screw-driver and hammer will also do the trick. After you have cut the circular hole in the deck, then you install the wood nailer to the deck fastned with screws. Make sure the nailer is the same height as the insulation you are butting up to, you may need to add plywood or double-up on the nailer to meet the height requirement.
So, at this point you have a round hole in the roof deck that is slightly larger than the flue stack. You have a square wood nailer that picture-frames the hole, but is held back about 1-inch on each side from the circular hole. The nailer should be wide enough to accomodate the base flashing flange, and should exceed the flange dimensions by approximately 1/2-inch on each side. The roof membrane has a small square hole cut in it, lets say approximately 8"x 8", with diagonal cuts at each corner so you could cut out the insulation and install the wood nailer.
If you’ve done all that correctly, you need to now install the flue stack. After it is in place, prime the top and bottom of base flashing flange and let it dry (you can do this before you start cutting and everything else, because it will take a while to dry). Once the primer has dried, take a trowel and coat the bottom of flange with a thin layer of flashing-grade roofing cement that you bought at a roofing supply store not the soupy stuff they generally sell at Home Depot, Ace, Lowe’s, etc. Set the base flashing in place over the flue stack and onto the roof. Using pan head screws, or roofing nails if you don’t have the screws, fasten the flange of base flashing to the wood nailer through the roof membrane. You will want to fasten each corner, and probably the middle of each side. Now you can install the torch-applied modified bitumen roof membrane. Scrape any roofing cement away from edge of flange where it likely got squeezed out while fastening the flange before installing the mod. bit.
At this point, I hope the torch man knows what he is doing. If not, let me know, but trying to teach someone how to torch-apply mod. bit. over the internet is probably not going to work so well.
Oh yeah, make sure you use pressure-treated wood for your nailer.
I didn’t read back over this, so if I missed anything I’m sure I’ll have plenty of people volunteering to tell me what I forgot. So I’ll leave it as it is, and wait to hear back from you if you have any questions, or need instruction on how to torch. BTW, make sure you take an all-purpose (ABC) fire extinguisher on the roof with you before you torch the membrane. Also, I hope the roof is asphalt and not coal-tar pitch. If it is pitch, you will know it by the way it smells like telephone poles (creosote aroma). If that is the case, becareful not to get the dust on you and try not to heat it up too much with the torch because the fumes will burn your skin.
Are you sure you really want to do this without a roofer???