Ok, let's try to answer this with the use of images.
But first, a little explanation. It is known from experimental evidence (and reported also on the wiki) that the Secret Rooms (the old ones, SR from now on) and the Top Secret rooms (TSR) have the following behavior: SRs are usually surrounded by 3 or 4 other rooms, while TSRs are usually found with a single room near them. There are exceptions, but we'll se them later. Also, based on my experience, a TSR is never found near other special rooms. Finally, EVERY level has both a SR and a TSR.
Now, to answer your question: which walls should you bomb to have higher chances of finding a secret room? Let's see some examples:
The first case is straightforward: we know that a SR has 3 or 4 other rooms around, and there's only one spot in the map like that. Bombing one of the red walls will bring you to the SR. For the TSR it's simple as well: while all the yellow-highlighted walls could bring you to a room that has no other rooms connected, they all belong to special rooms, so that leaves the green wall. So, in this case, with just two bombs you get both treasure rooms, as you can see in the following image: 
This one's trickier. While searching for a SR, you'll see that you have three spots that qualify, the two walls in purple and the one highlighted in red. In this case there's no way to tell which one is the real one, so you can waste up to three bombs while searching for the SR(the purple walls were the wrong choice, by the way). For the TSR it's even worse: any one of the yellow walls could be a possible choice, and each one of them would make you waste a bomb, because the green wall hides the actual secret room. The only thing that can help you here is your luck, unless you have a huge reserve of bombs, the X-ray glasses, or the Spelunker Hat when McMillen manages to fix it (it's currently broken and doesn't do anything).
This may be the trickiest case, at least the first 4 or 5(hundred) times you get it. Strong of your previous experiences, you may think that the purple walls are your best bet for a SR, and the yellow for the TSR. Sadly for you, this is the exception I was talking about earlier: the TSR can be generated with two rooms around it if one of those is a SR. Adding insult to injury, the TSR will count as the third room around the SR. Always keep a handful of bombs ready for these situations, and remember that both of the secret rooms are ALWAYS present in every level.
As you have seen, with both kinds of secret rooms, you always have to make some guesses, so having enough bombs(or Ipecac, or Dr. Fetus, or Epic Fetus) surely helps. Anyway, you can always narrow the possibilities by paying attention to the layout of the level. Also, the DLC brought a whole lot of highly dangerous new enemies that explode or shoot explosive bullets. Use them to your advantage, and lure them near the walls you want to blow up; saving bombs is always a good thing!
