Bees are endangered, so it's illegal to kill them unless they create a hazard -- but a hive in your roof soffits constitutes a hazard. A hive is heavy enough to create structural issues, and dripping honey can damage your walls and framing. Not to mention that bees sting, and they could start flying through your house. This doesn't mean you should kill the bees, but to permanently remove them, you must remove the hive.
Bees or Yellow Jackets
If you see bees flying in and out of a hole in the soffit, the first thing you need to do before taking action is to identify them correctly. They could be yellow jackets, which are actually a type of wasp that makes different kinds of nests. Yellow jackets have the same general coloring as bees, but they are hairless. The colony dies off in the winter and, in the spring, the queen will start a new nest elsewhere, so it's probably best to simply leave yellow jackets alone. Bees, on the other hand, keep building the hive in the same place year after year, and even if they leave, other bees will likely move in. The hive keeps getting heavier and more full of honey.
Assessing Bee Activity
Before preparing for a major bee extermination or relocation project, it's important to determine whether or not there is, indeed, a hive behind the soffit. The bees you see flying around may be only scouts. Spray the area where you see them with wasp or hornet spray, and wait for 15 minutes. If there is no more activity, you may have prevented the establishment of the hive -- keep checking back and respraying every two or three days until you're sure there's no activity, and then seal the hole with caulk. The continuation or increase of activity after you spray means that it's too late, and the hive is already established.
Funneling Bees to a New Hive
Although it's legal to exterminate bees that have nested in your house, it's preferable to relocate them, and most communities have beekeepers who are willing to do the job. A common technique is to construct a wire funnel around the opening the bees are using and place an alternative hive nearby. The funnel prevents the bees from reentering the house, and they join the new hive, which can be removed when all the bees have vacated the old one. It's a bad idea to simply block the hole the bees are using -- they will find another one, and it may be inside the house.
Removing the Hive
Once activity ceases around the hive, the hive itself has to go, or a new colony will start. You can usually disassemble soffits by pulling off the trim from around them and prying off the soffit panels with a hammer and pry bar. Hives can get quite large and heavy -- it isn't unusual for a hive to fill one or more 5-gallon buckets -- so secure your ladder well and be prepared to support weight. It's probably wise to get help. Be sure to scrape all the hive off the soffit and framing and to wash off the residue to remove the pheromones that attract more bees.