Comma separating subordinating clauses

Solution 1:

Your inclination to add a comma to the sentence between hill and and is an instance of wanting to use the comma as a marker for an omitted word or idea. In this case the omitted word is if, since the sentence's internal logic amounts to "if X and if Y, then Z." Such an addition can help with clarity in some cases, or it can be superfluous, depending on the complexity of the sentence.

But if you were to add a second if between and and Bob, I doubt that you would be inclined to add a comma before the and as well, since the parallelism between the first if and the second one would already be well established. Here's the sentence in that form:

If Jack and Jill were going up a hill and if Bob were simultaneously driving down the hill, Bob would run over Jill.

The decision about whether to add a comma or to add if or to leave the original sentence as currently written and punctuated is a judgment call. In this particular case, I don't think that any of the three options produces a bad result.