For starters, put doorknob covers on all the outside doors as well as the door to the basement and even your other child's room. Your 12 year old will be able to manipulate them and get in/out just fine. If you haven't already, put covers on the stove knobs if necessary. If the little one is a climber, be extra cautious. You can also put on one the inside of his bedroom door so he cannot get out - if he wakes up early, he can play quietly or he can go back to sleep. You can consider putting his bedroom light on one of those timers people use when they go on vacation - if he wakes up and the light is off, it's not time to get up yet (or at least not time to wake others up). Of course, the down side is, the light going on might wake him up when he otherwise would have slept, but you can take your chances.
If he can get over the crib rail, it's time to lower it to the lowest point - he won't roll out of bed while asleep. If he can get over the gates, it may be time to take them down. Teach him how to go up and down stairs - I used the 'on your belly' technique but some people use the 'on your bottom' technique. At this point, he's in greater danger falling over the top and falling a greater distance than he would if the barriers were lowered or removed. Depending on the design, you can also put a gate at the mid-point of the stairs - at least if he falls, he only falls for half a flight.
All you can do now is teach him safe techniques for navigating these hazards, since he can't be contained. Maybe your 12 year old can teach him - both boys might think it is fun - make a game out of it.
Good luck