I should note that there's no actual limit to Negative Qualities, there's simply a limit of how much karma you can get for them. You can easily take 29 karma in negatives, and only get 25 karma for it. Maybe you should simply raise the limit to 35 karma for negatives max instead, rather than completely removing it. Unless you also made clear you will veto ridiculous combinations such as Allergy: Severe, Sunlight, Distinctive Style, Corporate SIN and more.
For getting the team wet, it partially depends on the player composition. You can start with an extended version of Food Fight, or have them do some investigating and feed them some setting-stuff through bartenders (such as 'Yeah, some of my clients got busted here by a Megacorp the other day. Apparently they stole some gear of a guard they executed, and a Corporate Hitsquad came calling. Sorry about the damaged door, but insurance hasn't paid me back yet. Now what was that about Blondie, you have to get her to pay her debt?'). Make sure to get them used to a few big things:
- Excessive Looting bad (everything has trackers and if you steal expensive stuff that you weren't hired to, people want to send a message)
- Murder-hobos bad (unneeded killing just makes worse enemies instead)
- There's always bigger fish (there's dangerous guys out there so don't pick a fight you cannot win)
As for advice: Stick to mostly PR0~2 enemies at first, and don't throw Force 5+ Spirits at the party yet. Let people get used to the game before you start putting out stressful things. While it is possible to rival a PR6 in dice straight out of chargen, that's still not meant to be a fight you dare take on.
For rough shorthand NPCs: On their primary skills, 6+2xPR (so a PR2 goon would have 10 dice on their main weapon), 6+PR for attribute-rolls (so Reaction+Intuition just assume a PR0 goon has 6 total) and for secondary rolls (such as Perception). Don't forget mooks get their PR rating as additional bonus when resisting social rolls ('look, I believe you, but my boss needs me to check these things in detail').
Oh, one more thing: In principle, do not allow any negative quality that gives 10+ karma. These qualities are supposed to come with big negative consequences, and often a lot of it depends on the GM. A misunderstanding between GM and player here will easily upset people. For example, don't allow Corporate SIN until you're more experienced because it's a Negative Quality that requires a lot from both GM and Player. Without that careful balance, it's either freebie-points or an upset player. And feel free to ask us for advice on how to deal with specific qualities (e.g. allergy wheat/krill/soy means allergic to 1 of the 3 most-common food ingredients, so at least 50% of the food will have this normally).