Most the rails are pre-drilled at varying intervals depending on the product. Some of the plastic stuff is not drilled so you drill yourself. I prefer filling old holes with sea goin putty, some guys will fill with silicone which is ok too. If you use sea goin, drill out any old silicone used on the old screws so you get a clean bond to the fiberglass.
Screws depend on rail type. The type with the rubber insert should use a flat head screw. Non insert type generally uses an oval head as they look nicer and more finished. Stainless is preferred obviously so they won't rust and sheet metal screws are what you want because the threads run all the way to the head, wood screws have a unthreaded shank which is no good for this application. Size of screw again depends on the particular style of rail being used. I wish I had all this on the website so you could see but I don't yet. If you measure your old rail we likely have the direct replacement for it. A digital pic end shot and measurements helps too in id'ing what you have. Just give Brian a call here at the shop if you need info or help. 909-592-1000