Every rally rider develops their own routine over time, thru trial and error, shared techniques and brute repetition. The best way to learn is to DO.
How not to leave points on the table, (fuck up)? Simple. Read the rally pack.
Read the bonus description before you head there. Read it again when you get there. Follow the bonus requirements, take picture, record info, etc. READ THE BONUS DESCRIPTION AGAIN before you leave. Make absolutely sure you did what you were supposed to do, IN THE LOCATION YOU ARE SUPPOSED TO BE IN. (Giant bat on a building anyone?)
Assume nothing. If you're not sure, and you've read the bonus several times, CALL the RM and ask. Mistakes happen. Business hours change seasonally. Maybe the hours listed were winter hours and now it's summer. Maybe the item you're looking for really has been removed. You probably won't be the first to call if that's the case. If the RM can verify it's been moved, they will tell you. Otherwise you had better be sure you are where you're supposed to be and no one else finds the bonus.
The bonus is not complete until you do the paperwork. Don't leave the bonus area until you do the paperwork. At some point you may have dialed in your process and gotten good enough to write down the name of that river as you ride over it and remember to fill out the bonus paperwork at the next stop. But don't bet on it for the first several rallies. Stop, record the bonus, READ THE BONUS AGAIN, then when you're sure you did it right, move on.
You should always read the entire rally pack before you start to code or route the bonuses. You never know what trick the RM will have up their sleeve. Get a grasp of the points spread and general idea of what bonuses are like while you read. Make sure you read the foreward of the rally pack and understand how to apply the information there to each bonus. If a bonus lists the hours, but is labeled 24 hour available, you might want to double check that foreward and see how that applies to getting bonuses after the business has closed, when said bonus is listed as 24 hour available.
And if you get Leg X rally pack at a checkpoint, read it all there before you move on. Many a devious RM has put a bonus on page 2 or 3 for taking a picture at the checkpoint, during a small window of time. If you ride off to the the local McD's to sit and route, it will be too late to get that bonus.
Ok, so you're sure you're in the right spot. But you can't find the bonus. Look UP. Look way out. Look for any indication of a structure, fence, trail, etc. I was once looking for a "brass plaque mounted to a post" and could not see anything anywhere that remotely appeared to fit that description. It turned out to be a brass plaque the size of the top of a 4"x4" post cut off at a 45º angle. The plaque did not overhang the post. It was about 3' high in tall grass at least that high, 50' away from the parking area, over a rope 'fence' that bordered the parking area.
Another time I was parked at a bonus doing my paperwork. The bonus was to take a picture of your bike with 5 flags that were in remembrance of fallen LEOs. The flag poles are at the edge of the parking lot, and quite tall. I was parked maybe 10' from the poles. I'm almost finished when another rally rider comes tearing in, rides up to me, looks frantically around and yells to me, "where are the flags!?" The clock was ticking quite loudly at this point in the rally. I just pointed UP and he followed my hint, got off his bike and was taking his pic as I rode off.
If the sign goes into intricate detail about how much water flows over the dam every hour, read the entire sign before you start doing math. The verbatim answer might be farther down on the sign. If the bonus says to add up the height of "mountains", only add up the elevations of things on the sign listed as "mountains".
Don't discount bonuses that have a hike. They often don't take that long and are worth the points.
No plan is perfect. Be willing to toss out the plan and re-plan if it becomes apparent that you missed something or have fallen off your time line too much. In fact, plan to re-plan. Identify bonuses that you will cut out or add if you are down on time or up on time at a given spot in your route.
Every rally is different. Do as many as you can. Have fun!