Good questions. The directions that we are given change each year, but in general the base route is given out with pretty explicit instructions. Go here, turn at this town, checkpoint 1 is here and open from this time to this time, checkpoint 2 is here, etc. So if you decide to run the base route, then most of the large-scale routing decision have already been made, and in most years the bonus points are listed somewhat in proper order. I.E. as you're going along the base route, choosing to go after the bonus points will show up on the route in the appropriate order, and you can decide as you go whether you have enough time/energy and would get suitable reward for each of the bonuses. The ones right off the main road for decent number of points, sure, why not. The ones way off the beaten path for a gazillion points, sure, why not. The ones far away up a dirt path that you're not sure exactly where they are and aren't worth a terrific amount of points? Maybe those are worth skipping to save the time.
So when I get the initial instructions, first thing I do is identify exactly where all the required checkpoints are, and get them into the GPS. If you miss a checkpoint, you're screwed and everything else doesn't matter, so it's terribly critical to get that right before worrying about anything else. Next I start looking at the higher point bonuses. Are they worth enough that sacrificing some of the smaller bonuses will still be worthwhile? Does the ride out to them sound like it will be doable? Can I find where they are on a map within a few miles, and if I get closer am I likely to find it successfully when I get there? Any biggies like that get into the GPS. It's not critical to get an absolute address, and it's quite hard to get to that detail when quickly searching online or on a paper map. But usually just a town name is good enough for route planning later when you're playing with the GPS while en route. You only have an hour max from getting the instructions to being on your bike and heading out, so there just isn't time for perfection.
Last year's rally was split into two halves. The first half had only 8 stops. More you got to the more points you got. Some were time-limited, some weren't. I managed to get all 8 into the GPS before I headed out, and then just rode them in order, skipping ones when I realized time was running out. Second half was more traditional, with a detailed base route described along with dozens and dozens of small to mid point level bonuses. A number of people chose that route, a few people including the rally winner managed to pick up virtually all of them, and that was enough points to win. There wasn't really an optional route in the instructions, but there were 5 or 6 huge point bonuses available if you were willing to ride a pretty great distance during the second leg. I tend to prefer that compared to getting on and off the bike several times per hour chasing smaller bonuses, so I chose that one and was on my way for the second 12 hours. Before setting off I took some time to identify the ones I wanted to get and their point values, entered their location as best I could into the GPS, sometimes by town name only, and that's how I rode the rest of the rally. I've got 2 GPS's on the bike, and one of them is almost always aimed at the next checkpoint or in this case the rally endpoint, so I can keep track of how I'm doing on time while I'm chasing the different bonuses.
Everyone has their own strategy, and it is going to differ depending on how the instructions and the rally are both structured. These change every year just to make it interesting. One year the base route was handed out on one set of instructions, while all bonuses were handed out on a completely different set of pages, and they were in no particular order. Was hard as hell!
You had to figure out where they were, then you had to figure out if where they were was anywhere close to the route you planned on taking, then you had to decide if you wanted to change your route to get closer to particular bonuses, but that could make it harder to get others if you hadn't yet located where they really were yet. Really was quite a mental exercise, and I don't think it was one of my best rallies.
To answer your primary question in the simplest way though, as a complete newbie what I would do is concentrate on the checkpoints alone, plan on staying as close as possible to the base route, and picking up bonuses that appear doable without endangering the first two goals (checkpoint / base route). Some people ride their first rallies doing nothing but the checkpoints, but often once they get into it during the day they change their plans slightly and start to go for points as their competitive nature kicks in.
