Don't feel like you're the only one wondering about this issue. I've read many, many posts about it.
I'll try to make it clear to you.
Q:
I have never pruned one of my plants before. To my understanding, you wait until it has it's 3rd node and then clip above it?
A:
No. You should never prune an MJ plant until it's reached sexual maturity. This is when the plant first develops alternating nodes on it's primary stem.
Q:
by <pruning> it will then split into two tops?
A:
Yes. If you perform what is commonly known as "topping", it will cause the one stem you remove to grow two stems from the same location on the plant.
Q:
Will this create a problem with me growing K2 which is supposed to be a short, compact plant?
A:
No, the result of topping will cause the same result in any strain except lowryder. With the lowryder strain, it will cause problems and is unneeded anyway because of that strains characteristics.
Q:
Also, does this ultimately yield more in the end, and if so, how many times should it be pruned?
A:
The end yield of an MJ plant is a difficult concept for many to understand. There are many, many variables involved. IF two plants are allowed to grow outside under the same exact circumstances, and one plant is pruned however many times, and one plant is allowed to grow naturally, and both are allowed to grow the entire season, then both will have the same amount of weight in buds when cured. This has been proven so many times in lab environments that it's become redundant in it's extreme.
However, and this is the BIG, HUGE, however, if the plants or plant is restricted in some way indoors, and full height is not an option, then a pruned, or topped plant will result in a larger yield if allowed to reach a height of 5 feet. If another plant is treated exactly the same except for having no topping and allowed to grow only to 5 feet, then it's yield will result in less weight of bud because of a restricted growth height.
In other words, if you were to allow two plants to grow outside in natural sunlight, and you topped one ten times, it would end up being shorter and bushier than the plant you allowed to grow without topping. One plant would be maybe 6 feet tall and 6 feet across, while the other would be 20 feet tall and only 4 feet across with much less side branching.
Both plants would have almost identical amounts of cured weed after harvest at the very end of the season.
Pruning or topping is done on inside grows to maximize the yield indoors.
Pruning or topping is done on outside grows to help disguise the plants and prevent them from being seen by unwelcome visitors that may not like MJ.
I hope this makes the subject more clear to you.
Good luck to you!