As someone who uses the IS capability of the EF 100-400mm L series lens a lot, I can say that it is something you need to choose to use. IS is a tool, and it is designed to solve a specific problem. Its not the ubiquitous hammer that can apparently solve every problem known to man, so you need to be explicit about the cases where you use it.
IS is intended to improve the performance of a lens when hand held, in situations where hand-holding is either not possible, or difficult. If you have enough light to follow the
Focal Length Reciprocal rule, which states that a shutter speed of 1/FocalLength at a minimum (without IS) should be used to capture a sharp photo, then turn off IS. If you do not have enough light to capture a sharp photo at a proper exposure with the reciprocal rule, then you should enable IS before you increase the ISO. The IS system of the 18-55 might get you 1-2 stops of additional hand-holdability, while better IS (such as that on the 100-400mm) may get you up to 3-4 stops additional hand-holdability. That means you could reduce the shutter speed up to two stops lower than the reciprocal rule would dictate, and get a clear shot. At 55mm, that would mean a shutter speed of 1/15s (+2s tops) should be sufficient. At 400mm, that would mean a shutter speed of 1/100s (+3 stops).
If you are unable to get a shot by enabling IS, then its finally time to crank up your ISO. As a general rule, I try to keep my ISO as low as possible. In the case of shooting wildlife and birds, I tend to set my ISO to Auto, and unless I'm photographing in bright daylight, I turn IS on in mode 1 (stabilization in both horiz and vert planes.)