You can apply everything from side view, except you have to translate depth according to your isometric projection. What helps me in this case is think of having a light above the character and imagine where the shadow of the foot will be on the ground. Then, draw a line up from the shadow by the amount it would be off the floor in side view. You can apply this for any joint on the body (knee etc) to figure out where it needs to appear in this projection.
Another way to do this translation is to place side-view keyframes directly into your scene (copy-paste), and then use skew transform to place it in side view in isometric. Imagine this is a slice going down the middle of the character. Then, instead of going floor up, you extrude joints left and right from this middle slice, following isometric projection (so the lines will go diagonally down-right, and up-left). You need to do this for all joints that are not in the middle plane (hips, knees, foot, shoulder, arm). Spine and head joints remain in the center. Do this for all the frames of animation (just drawing lines between joints) and you should have a proper skeleton base in isometric.