Regarding fit:
There are really only two things that have to be positioned: the saddle and the bars.
The bottom bracket is the starting point of everything. The saddle is the first thing to be fit. Most people use the old knee-over-pedal-spindle method. There are arguments that it is only an approximation, but I've used it for years and have had great success. Since I remove my saddle for packing and I travel frequently with my bike, this fit step is something which I repeat often. The process is as follows:
1. Set your saddle height so that when your pedal is at the bottom position and your knee joint is locked, the sole of your foot is paralle to the ground.
2. Move your pedal to the forward-horizontal position. Take a plum bob off your knee. Adjust your saddle fore aft position until the line passes through the pedal splindle.
3. Check your saddle height setting again in case it has changed.
For time trial bikes, the knee should be forward of the spindle; for mountain bikes, the knee should be backward from the spindle. I don't ride these disciplines so I don't have the numbers memorized.
Once the saddle is positioned, your lower body fit is fixed. Only your arms are left. There is no correct position for the bars. Your setting will depend on your fitness, speed, and preference. Generally, the lower your bars, the shorter the stem. High level cyclists will want bars which are lower and more forward than casual cyclists. Bicycle tourists usually prefer high bars. The bars on my touring bike are just slightly below the saddle. The bars on my road bike are 10 cm lower than my saddle.
To summarize, the saddle position is based on the bottom bracket, and the bar position is based on the saddle. Pretty much any manufacturer's frame, when reasonably sized, can be made to fit any cyclist with the correct choise of stem. Frames are traditionally sized by the seat tube length, but the more relevant dimension is the top tube length. When the frame size deviates enough that an especially long or short stem is required, handling become compromized.
You should consult a competent fitting professional if you purchase a mass produced frame. If you opt for a custom, your builder should take care of this for you. If none are available in your area, use one of the available online calculators to determine your frame size. Leave your steerer uncut. Once your frame is built, start with the bars slightly below the saddle, and experiment with stem lengths until you achieve a comfortable position. The problem I see the most often is people riding handlebars which are too far forward. This leads to hand, back, and neck pain.