I'm not sure about your first question, but I've done a fair amount of research involving western blotting and SDS-PAGE. Basically, your primary goal in western blotting is to quantify the amount of protein within a given sample. The cell parts are not important to this, so you take your tissue sample, homogenize it, water it down to a concentration that can be read by whatever protein assay you're using, and then add a protein stain to it. This stain will be useful later for determining if your sample has finished running. You use a Pasteur pipette to put the sample within the polyacrylamide gel wells. Once placed on the rack holding the gel, you place it into this contraption that runs a current through it, along with some buffer solution. (Sorry I'm not too clear on the terminology in English - did the research overseas ;D) You have to make sure the voltage is the correct direction. Higher mass samples will run more quickly than lower mass samples. This is when you watch the protein dye - as it moves, you will see faint lines forming on the gel. Wait for an hour or two or until the lines have reached 1 cm from the bottom. After this part, you take apart the rack holding the gel and place it onto a transfer membrane, carefully, while sandwiching it between foam and some plastic clip that keeps everything together. Place the appropriate buffers to keep it from drying out, and run it in another contraption for an hour or so. Take the transfer membrane out, discard the gel, and develop the film. Western blot analysis will reveal lines showing where the protein has moved, thus allowing us to quantify how much protein was in the sample.