Several of my magic users are coming up on the chance to join magic groups to initiate. I was wondering how everyone out there handles the mix of magic user in a guild and PCs that are not and running the shadows?

my group generally start one as soon as possible. we generally recruit random magic users until we have around 10-20 people in the group. just dont associate the magic group with a shadowrun group.

"So, what do you do for a living?"
"I'm not currently working, but my trust fund hasn't run out yet, so I'm hanging in there. You?"

If the PC has too much of a gutterpunk personality, he probably wouldn't even be allowed into a group where it would be a problem.

Do you use the groups for a lot of role-playing opportunities, or do you just wand-wave a lot of it? If the former, play it out and see what happens. If the latter, don't worry about it. Either that, or let it ride for a bit, and then make a role-playing opportunity out of it.

I think it depends on the situation. At times i would just narrate the magical group based situation and at other times make the player role play through it. Like if its the same old same old, then i would just glance over it, but if its something like in house revelry then i would play it up.

I don't think most law-abiding citizens would like the idea of having hardened criminals in their midst, so it's a valid concern. Come up with some groups and see if the character wants to join. You'll have to decide how hard they have to work to fit in, and they'll have to decide how hard they want to work to fit in. Like you said, sometimes this can be established with a conversation, and sometimes it may need to be acted out. And you'll decide how much conflict you want there to be.