My general advice is just to taste your food as you cook it. Start with a little hot pepper and figure out the "heat level" you like, with whatever peppers you use, and then you can add more to calibrate the recipe. Keep in mind you can always add more spice with more peppers, but it's difficult to lower the "heat level."
If you can stand to taste the peppers directly, you can also use that to get a sense of when you might have a hotter or milder batch. I'd probably start with 3 to 5 jalapeños to substitute for a habanero, but it'd depend on the recipe, the size of the peppers, and the spiciness of the batch.
In terms of flavor, I find habaneros to actually be more "fruity," but it's hard to experience that since the heat is so intense. Jalapeños are more "vegetal" and "bright" in flavor, more like a bell pepper with some heat. If you want chunks of juicy hot pepper in your dish, jalapeños are probably a better choice.
An exact conversion is impossible here. Peppers can vary quite a bit in size, and different varieties of jalapeño or habanero can vary significantly in hotness (in both cases, the hottest varieties can be at least 5 times as hot as their milder forms).
Roughly speaking, habanero peppers are about 50-100 times as hot as jalapeños (on the Scoville scale). But that's in terms of density of heat, which may be very roughly correlated with heat per unit weight. (Traditionally the Scoville scale was based on empirical tasting methods that were quite variable, but more recently the American Spice Trade Association (ASTA) scale has adopted a more precise method based on dried chilis and chemical measurement of spice components. But the ASTA scale also has limitations since it is based on dried samples, whereas fresh peppers are mostly water.)
In any case, since habaneros are much smaller and thinner than jalapeños, it's really hard to come up with an exact conversion for equivalent heat. My personal experience would suggest that you'd need several jalapeños to equal one habanero, but it's really tough to judge. Many supermarket habaneros I've had seem quite mild: I could add several to a large pot of chili and still find it not excessively spicy. But I've also had homegrown habaneros that were so hot that even one would make a pot of chili barely edible (to "normal" folks who aren't into excessively spicy food).
In general, I agree that the juicy, larger fruit of jalapeños is often desirable. I tend to use them in a dish where I want the crunch or taste of "peppers" in addition to heat. With habaneros, unless you want really spicy food with a high concentration of them, you're not going to taste the "pepper" elements -- it's more like generic "heat." I would just be very careful to chop habaneros very fine. (Also, use gloves and do NOT touch your face.)