Hi Leor!
To quote a good friend of mine, who also happens to run a fairly large convention, when asked the same question: DON'T!
That is of course a bit of a cynical response, I really don't want to discourage anybody from starting something for the good of the community. But you need to be prepared to go to a lot of grief and pain, since getting your own event off the ground is really, REALLY hard. You need to find a team to start with, and you also need to find an audience to attend your event - which is especially tricky if you're not a well-known name among the people you're trying to attract.
To make things even worse, there is no strictly "right" or "wrong" way to do it, so if you had hoped that I can point you to someone who can basically take your hand and guide you through the process, I'm afraid I have to disappoint you. However, If you have any more specific questions than "how do I run a con", I'll be glad to answer. And since a lot of staffers read this forum, others may chime in every now and then, too, if they're interested.
As a general piece of advice for someone new to this business, I would say: Start Small. Try running something like a furry BBQ event, or something to the extend of a large birthday party. At first, you won't be able to attract a large number of people for your first event, anyways. You'll basically have to start with people from your own circle of friends and acquaintances, maybe in forums where people know you. Those are the people who trust you, and might be willing to attend an event you run. See how many you can gather. If you know a lot of people, maybe you can even rent a small location, like a youth hostel or a camp ground, and make some initial experiences with the logistics of a larger party. But anyway, don't plan for 200 people on your first event.
As for the charity bit - if you're planning to collect money, that is something that will only make sense if you either have a really small charity (like, supporting the good cause of one single person), or a more substantial number of attendees. I mean, a good charity will appretiate any donation ... and even if it's just €10. But on the other hand, don't expect a medal of honour for it
You'll have a hard time getting people to attend your event in the first place - and motivating people to donate any substantial amount is really hard work, and that work will only really pay off if you have a few hundred attendees to work with.
Of course, collecting money from your attendees is not the only way to be charitable. You could, for example, organize events with fursuiters attracting attention for charitable causes - the classic is, go to a children's hospital in fursuits. Or, help a charitable organisation by providing fursuiters as mascots for their own donation drive in the city. You can be very creative. But of course you'll first have to find out if they feel comfortable with that kind of attention, and choose wisely who you'll send there - knowing how socially awkward some members of our community sometimes can be.
Another good reason to start small is that, for any larger event, you also need a large team - and you can't build a large team out of thin air over night. It's the most painful part of running a con: Building a team and keeping it together. In terms of challenges, this is MUCH harder than running the actual event, and it is always underestimated. Most new conventions that fail don't do so because of mismanagement of resources. The do so because of the team breaking apart.
Working with volunteers takes some serious leadership skills, and you will have to acquire those skills by trial-and-error. (Well, unless you're a trained manager, but if you were, you wouldn't be asking these questions.) I can't stress this enough: Building your team is the hardest part. Finding people who share your vision and goals is hard. When you start out, everyone has different motivations, no matter what they say. Finding people who are willing to admit their mistakes, and learn. Finding people who you can depend on, and who actually go through with what they have promised.
Don't try to be a con chairman, if you are not prepared to fire your best friend.