Where are you playing? In Their World or your own city?
What are some creative ways of getting the characters together, working as a group?
How well does the game run if people have to run off in pairs or individually?
First hate term DMing. Means when I look at it dungeon crawling with no creativity to gaming. Just Rollplaying and Hack and Slash. It is best to think Game Mastering or Storytelling the approach is different as the GM.
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I am running my game in New Mexico in Modern Day, Albuquerque.
One of the best ways in Dresden Game is the City Creation system. The players and GM build the city together and at least all my players seemed to start working on how the group would work making it part of the background of our city.
I am a White Wolf Storyteller since First Edition Vampire hit the shelves. Getting parties together is easy for me in the Dresden Game. Mutual Enemy, forced by design, etc. Even starting out in a Nightclub (*cough* tavern in D&D terms) can help.
I find even building characters at the same time helps with the group being formed helps/
I find nitches in backgrounds and Dresden forces a background even for the most Roll styled player that thinks backgrounds don't help.
Aspects are another way to do it. Even Guest Staring some of my players even Guest Stared in each other's origins.
My players all decided on their own that they would be Bounty Hunters for the Unseelie Accords. Not what I was expecting but works great with how we all built the city together.
Now you ask about soloing part of a story and if the group breaks up how to handle those instances.
Simple run it. Here is some examples I do:
If Jan The Werewolf is not in the scene because he is off doing a computer hack while Valeria the Wizard and Jack the Kineticmancer have to go meet with Manuel Esteva the local Drug Kingpin/Red Court Vampire. You run the scene. Not that hard. Jan's player sits back watching the scene while you run it or he goes gets a drink, grabs dinner for the group etc. Most players I know watch to see what happens.
Then when done you run a scene with Jon, maybe while he is hacking. Bear the Agent of the Archangels shows up just before a bunch of ghouls attack. Or maybe Jan and Bear are dating or Jan is secretly in love with Bear (an Aspect Jan Has) that you can run with.
Never had a problem splitting parties. As a White Wolf Storyteller that happens a lot. Just make sure you give everyone good time.
Another thing I do if a solo session or two member team session is to start the next game. I have the player(s) show up earlier that day or show up earlier in the week so I can run the scene with no one there.
Sometimes when I do a solo, I take X-player in the back, lets say the computer hacking Werewolf Jan and tell her some juicy tid bit she discovers through her extensive action. So she holds on with the information as I run Valeria and Jack through their scene with Manuel then tell Jan this is when you found the information (not saying what it is so Val's and Jakc's players do not know) and what do you do now/
Honestly never had an issue splitting up the group in any of my games actually sometimes it helps drive the story better and can cause great roleplaying scenes.