It is generally accepted practice to declare Directed Targeting for most volleys, especially when there is a chance of a burn-through point. The idea is that when using Directed Targeting, you have a 50% chance of your burn-through point hitting an "important" system of your choice: weapons or power, which are, generally regarded as "important" systems. Because of this, it is usually considered preferable to include no overloaded weapons in a volley where you expect burn through, in order to allow directed damage. However, there is more to it than that. Please allow me to explain.
     If you declare "targeting power", there is actually a 67% chance of your burn-through point hitting something important, just so long as you don't mind whether it's weapons or power. If you roll a "one", a "five", or a "six", you will get a power hit as usual - fair enough. However if you roll a "two" you will get a phaser hit - still an important system and much better than lab or transporter. However, if you target weapons, there's still only the standard 50% chance that you will get an important hit.
     And there's more. Because you can hit a phaser on a "two" or a "six", and a warp engine box on a "one", there is still a 50% chance of your burn-through point hitting something important even without using directed damage, just not something that is necessarily your choice.
     This means that a burn-through damage point always has at least a 50% chance of scoring an important hit, whether it's targeted or not. Therefore, if the odds are not good that you will score a burn-through point this impulse without using overloads, you should actually go ahead and use overloaded weapons. You have the same 50% chance of scoring an important system hit with your burn-through point as you would if it were targeted. You should therefore feel free to use overloads if by doing so you will get a burn-through damage point, even though you can't target that burn-through point. The odds are pretty similar, and pretty good, whichever way you do it. Also this allows you to overload, say, your one disruptor, rather than using two, allowing you to use your unfired weapon later.