Here some extra advice for you...
First of all preparation is your best friends, especially if you are a beginner at GM. Prepare as much as you can the crunch - you can go as far as roll the initiative of your bad guys in advance, and roll their first tests (and thus decide what will be they "most likely" first actions). This will free you of some thinking during the game.
Also, ensure (as mentioned above) that your PCs are implicated and also have a part to play. For each scene, go over your PCs characters: If there is a Face, prepare some skilled social interaction, if there is an Awakened, think about what can they see in Astral or feel as a magician, if there is a Weapons Specialist / a Street Sam think about what this kind of character will see during the scene.
Also don't write the "story" and don't script too much a scene. This will give an impression to the player of being railroad. Instead, prepare how the event led to the specific scene, what are the plan and motivation of the factions in play. Quick exemple - your next game starts with the PCs going to discuss with a Mafiosi who seems to have some information they need.
Scripted Scene: "PCs comes in to discuss with the mafiosi capo, who dislike them quickly, end up in a shooting contest and the PCs leaves with the commlink with the infos they are looking for once they have defeated the guy"
A lot of things can go wrong here: a Face character can roll incredibly well, making it very frustrating for the PCs if the negotiation goes side away, the group's hacker can brick the commlink, or the group can simply forgot to pick his commlink up. Here is a better approach:
The mafiosi is not friendly and having a bad day (prepare the crunch associated to "hostile social interaction", to have the penalty to give your player handy, if nothing else give the NPC a Charisma, Negotiation and Intimidation) - why ? Let's day a deal just went badly and some KE agent busted his last shipment of BTLs, so he is pissed, and a bit paranoid (someone HAD to tell the cop).
What does he want ? To know what happened or to exact vengeance to whoever thinks he is behind this. So if you PCs led the discussion into this direction (either by chance or by rolling extremely well), they may be able to make a deal. Otherwise, you have your original shout out scene.
Now, let's think about PCs
implication in the scene - first of all this scene will start as a (difficult) negotiation. Perfect for the face (if any), but what about the other characters ? Think about involving them (prepare the crunch: check their character sheet for possible teamwork with the Face). First think about hackers (what can they see, which device is running silent or not, how did the mafiosi build their Matrix security - most likely they have a PAN for all their device, but where is the device running the PAN ? What is its rating), and Awakened character (what can they see in the Astral ? Which kind of Spells is already running on the Mafioisi.
Let's say you have a Decker and a Mage - you want the group to not be completly vulnearable on both side, so the Mafiosi may have a low Force spirit around, as a courtesy of a Mage allied to the criminals, and maybe a decent commlink (DR5) hidden on the "biggest" goons.
Now think about the other characters: The street sam might be able to ready the body language of the criminal - or at least notice which kind of weapon or augmentation the mafiosi have (thus feeding the infos, during the negotiation about their threat level), but also may be able to provide interest intel thanks to his Knowledge Skills (especially if they relates to criminal organisation). Maybe, with a decent roll, he may get the feeling that the group just had something bad.
Other piece of advise: if you the scenario involves some investigations - and IMHO, a good Shadowrun story should
- you can make your life easier by making a list of their contacts and for each prepare what would they know about the events. Try to find, for each, either a piece of information, and if not, a lead.
Ex: Your group is investigating the so-called accidental death of a Neo NET exec in a, apparently genuine, car crash. Story behind it, the exec manipulated a group of mage and they sent a powerful spirit to use its Accident power on his limo.
Contact 1: Corporate Agent - this one might know part of the story, like how "lucky" the dead guy was (thanks to the help of the Magical Group)
Contact 2: Talismonger - he may be aware of a recent summoning of a large spirit because some reagents were massively bought around the same date.
Contact 3: Barman, OK, this guy may not have any relevant infos, but he might now for instance an other Neo NET suit who was working in the same building or branch - maybe this guys will know something (see Contact 1).
Last piece of advice - check a bit what your player want (try to understand what was "OK" or not, but not really in terms of "you could have done this or this better", but more in term of "this story was too much action or too much investigation").
So, whenever you prepare a story or a scene, double check it with the following question:
1) Is the factions in play and their motivations clear ? Do I know what led to the scene and I am NOT railroading its resolution ?
2) Are my PCs invovled here ? Do they have a role to play ? Does all PCs have a part in the scene ?
3) Is this the kind of scene / story they actually would like to play ? Does it matches what they like (or disliked) ?
