Heh, my first advice would be "don't allow 550BP characters your first time out."
I'm kidding, of course. If those are the characters they want to play, they certainly need those BP. Here are some thoughts for you:
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1. Are there any good map making programs around for Shadowrun?
Personally, I avoid relying overly much on maps. The Shadowrun rules do include some relatively abstract movement rules and such, but I find that the game runs much more smoothly if you focus not on visual representation, but on what the characters are actually trying to achieve. I know that sounds weird, so let me give you my favorite example of this.
Situation: Dark night on a busy pier where lots of shipping occurs.
Now, do I spend a bunch of time looking up a suitable map, or drawing one? Nope. What I do when combat breaks out, then?
Example fight: A small team of security guards that the 'runners' intel didn't mention has caught them, and it has escalated into combat.
Player A: I run right and take cover behind a shipping crate!
Examine for a second what this player is actually asking for, tactically. They want the cover bonus (aka penalty for the attacker's pool). So do I need to look at a map and find out if there's a shipping container? Nope, it's a busy pier, so those are likely to be scattered all over the place. What the player is doing is thinking tactically and creatively, so I reward that: BAM, they have a shipping container to hide behind. The guy shooting at him now has a tougher time.
Player B: Is there any kind of drone or anything nearby, maybe a remote controlled forklift that I could run a guard over with?
Again, no need for a map, you just apply reason, and more importantly, you reward the player for being creative.
GM:Yup, (remember, busy pier) you scan around and find the node of a container carrier drone.
And yeah, you get to do this for your NPCs too.
Anyway, enough rambling on that. Obviously this lends itself to one style of play, and maybe not so much to others. If you do want a highly tactical, movement rules type game, it might not work as well for you. Whatever gets your players into the game is the best way.

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2. My group consists of a human face adept, a drake chaos magician and a vampire infiltrator. Seeing as how none of them can really spare the Karma for non-magical purposes and the rules on agents are fragging impenetrable, how should I go about the Matrix with them?
The stuff for agents, while a bit daunting at first, really isn't that bad. Basically, and especially if your players are using them as almost an NPC hacker, think of it as exactly that: an NPC that does hacking for the players. How far out you want to abstract it depends on how important it is to you, your players, and your game. You can go all the way from following the Agent and Hacking rules to the letter to waving your hand and saying "your Agent comes back with the information you wanted." It all depends on what you guys decide you want.
You can also use contacts to solve this issue. Stat up, look up, or just wing an NPC hacker that one or all of the characters knows. You can even use this as a resource management tool, since hackers typically aren't working for free.
Nothing to add on magic in a suborbital at the moment. I'll post it if I do think of anything.
And good luck!