Concealment does indeed work on non-living things like cars and such. An easy way to limit this power is to say it won't work on anything with a body more than twice that of the magic of critter using concealment. so to hide a bulldog van (Body 16), you would need at least a force 8 spirit. This is basically the same as the rule for the movement power. Of course, if someone used concealment on the Space Needle you would notice right away anyway plus the building is still there so it wouldn't work all that well. This power is intended more for things that can move rather than stationary objects that have an address. It is also very effective for use against the search power.
Astral Perception can only be used to target astral things, so unless that chameleon suited target is also astral, the magician can't target him. Keep in mind you can use edge to make long shot tests so even with a pool of 0, you can spend edge to roll your edge dice and still possibly succeed (exploding 6s). Also remember, even an pool of 2 dice can succeed if the chameleon suited dude had a crappy infiltration test. If he isn't hiding at all, the threshold to spot a guy in that situation is only a 1, so still possible. Chameleon suits aren't invisibility suits. You still need to make an effort to hide, they just make that effort more effective.
Managing karma/cash can be tricky. The 1:2500 rule of thumb is a good one to go by and if you aren't getting close to that for payouts, you need to bump up the cash people are getting paid. For things like snatch and grab I like to use a 10% rule, that is for the object or data or person being snatched, the Johnson will pay out 10% of its value to the runners. More than that and it stops being as profitable. So if the team is hired to snatch a new million nuyen bit of code, the Johnson will offer a max of about 100,000¥ (the team would negotiate up to this), with maybe 75,000 as the starting offer. This would be split between the team. For other jobs, like assassination, if it requires the whole team, then they better pay for the whole team. Today you can get someone offed for around 25,000 I think (someone tossed that number out before) so don't expect your runners to do it for 5000¥.
If you look at some of the Missions, they offer some pretty good payouts. SRM-01 offers 7000 per runner with a negotiation test adding 500 per net hit (max 6) to recover some guy hiding in the ork underground. This can end up being 10,000¥ with max hits, which isn't bad and there can frequently be chances to get extra cash (stealing gear and fencing it, counter offers from other parties, etc).
Ultimately, you just need to get a feel for it through experience. This will take knowing your players and their characters and who needs or wants what. The magician has his eye on a power focus? Well how many runs do you want him to do before he gets it? This will give you an idea of how much cash and karma to hand out. Samurai wants to upgrade his wired reflexes? When do you want him to do that? Well that tells you how much cash he needs. Adept looking to grab a new power and needs to bump up his magic? How soon would you like to see that in game?
Of course it is also a really good idea to ask the players how soon they would like these things and then, after they say right now, try to come to some reasonable compromise.
Remember good roleplaying can earn extra karma you may not have factored in and clever players may come up with revenue you weren't planning on but generally it isn't enough to upset things too much. So the mage got his focus one adventure sooner than you had planned? No big deal. He might get one adventure where he has more of an edge than usual but you can scale things pretty easy in this game to compensate, even on the fly.
Don't forget to factor in their lifestyles and other expenses (magical group dues, pirated software upkeep, etc) to their payouts as well. Starting out they will probably have low lifestyles and as they gain cash will want to upgrade (who wants to live in a slum if they have a choice?) to higher.
Hope this helps.
