The entire difference is in sign conventions; the sign merely depends on your method of thinking on how the system does work on its surroundings.
In the formula delta u=Q-W, W is positive when the system does work on its surroundings and negative when the surroundings do work on the system. For instance, if a balloon is heated, we gain heat (+Q), and the balloon expands, doing work on the surrounding atmosphere (+W). If we would plug this into the equation, we find that the change in internal energy equals the gain of energy from heat minus the energy lost when the system does work.
In the other equation, delta u=Q+W. In this equation, it is assumed that when the surroundings do work on the system, the system gains energy and W is positive. When the system does work on the surroundings, the system loses energy and W is negative. In our expanding balloon example, then, we have energy gained from heat (+Q) minus energy lost through work done by the system (-W).
Either equation works as long as you remember the sign convention. Personally, I prefer the Q+W formula because I find it easier to remember that +W means gaining energy and -W means losing energy, but that's just me. Hope that helps clear things up.