That's really entirely up to you and the type of game that you and your players wish to play. Many DM's (often including myself) never roll for random encounters. For myself, at least , this is because I prefer to look at combat as part of the storyline, rather than just the reason why averyone is here. If people were only intereseted in the combat encounters, which having unplanned, random encounters emphasizes and greatly increases the numbers of, then they could play a computer game like Diablo which has a much better and quicker engine for resolving combat.
I also prefer to plan the encounters ahead of time so that they can be more tailored to the area that the party is in and the power level/ability of the party.
This is not to say that I never use random encounters, just in specific situations. For instance, there may be a large swamp that has a shambling mound living in it. Quite a threat to a low level party. If the party spends a lot of time in the swamp then I may decide to let the dice choose whether or not they meet him. Likewise, if they are trying to sneak into a military encampment, I may roll the dice to determine if they walk near a patrol.
But these are all specific, predetermined encounters that I am simply deciding when and if they take place and I'm not worrying too much about the numbers.
As for the difference between rolling 12% 3 times or 36% once, it is certainly the former. If it were the latter then there would be a guaranteed encounter every 9 hours and that is far from realistinc.
Random encounters are a tool that the DMG gives to you, but you should use them or ignore them as you feel appropriate. If they add to your game, then make the best of them, but never let them run the game for you. Ultimately, it is your game, not the books.