Making a downstem is straightforward but getting it right the first time takes some patience.
The whole point of a downstem is directing smoke through the water chamber so you get proper filtration and cooling. A poorly made one will either restrict airflow so badly you can barely inhale, or leak water into your mouth because the seal doesn't fit. I learned that the hard way on my first attempt. You need four things: a piece of glass tubing that matches your bong's joint size, a glass rod or thicker tubing for the stem itself, a glass cutter or rotary tool, and a torch. Most bongs use either a 10mm or 14mm female joint, so measure before you buy anything. Miscalculating that once cost me about $30 in wasted supplies. Cut your stem tubing to roughly two inches in length. The exact measurement depends on your bowl height — you want the bottom of the downstem to sit about a third of the way up your water chamber. Too short and it doesn't submerge enough for filtration. Too long and water gets sucked up the tube when you inhale hard.
Next, take your glass rod and heat the end until it softens. Push it into the cut tubing until you have about half an inch sticking out the bottom. This is your intake end. The top needs to rest flush inside the joint opening so it doesn't rattle or pop out during use. I burned my fingers doing this step and the fit was terrible on my first try. What I ended up doing was using a sanding disk on a rotary tool to taper the top of the stem so it seated snugly against the joint walls. It took about twenty minutes and the seal was solid. Fire polishing is the step most people skip and regret later. Run the torch over every cut edge until the glass goes glossy and smooth. Unpolished edges crack under thermal stress and they're rough on your hands when cleaning. If you're working with borosilicate glass, it handles heat better than soda-lime, but polished edges still prevent micro-fractures from forming over time.
Check your fit by dry-assembling the downstem into the joint. It should slide in without forcing and sit level with the bore. If it's recessed too far, your water immersion depth is wrong and you'll get harsh hits. If it sticks out past the joint, it'll catch on things or fall out when you move the bong. When you actually light it, watch for water traveling up the stem. That's called backpressure and it happens when your water level is too high relative to your inhale strength. Lower the water level a quarter inch and you'll usually fix it. Some people add a tree or percolator diffuser to the downstem itself, but that adds complexity you probably don't need as a beginner. A homemade downstem will never be as perfectly sized as a factory-made one. The gap between your hand-cut stem and the joint walls might allow a small amount of air to escape around the top, which reduces draw resistance slightly. If that bothers you, you can wrap a thin thread of glass around the top before firing it in, building up the diameter until it's a tight friction fit.
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I've been putting together these things for years and my current go-to setup uses a 10mm arm percolator downstem bought off eBay for about eight dollars. The homemade ones work fine, but if you're doing this regularly, the cost-benefit shifts toward buying pre-made unless you enjoy the process itself.