Saving the best (worst) for last, I'm deciphering PERMISSIONS!
1) Admin permissions within the Admin CP itself are defined separately from the user groups. They are located here:
Admin CP -> Groups & permissions -> Administrators
On the other hand, user groups control permissions on the front end. Admins still belong to user groups because they have front end permissions as well.
XenForo's standard usergroup organization is to have everyone as a primary member of the Registered group to define a base set of permissions which are common to all registered logged in users. Then secondary groups like Administrative are added to confer additional front end permissions as appropriate.
When you import from vB it preserves all of the vB usergroups and group memberships which might not be organized the same way as a default XenForo installation. For example, there may be users which are primary members of groups other than Registered. That's fine and it will still work. But since newly registered users will be made primary members of Registered I would normally recommend being consistent and using that same kind of group organization for everyone.
2) The imported Subscriber group will have the same permissions as in vB since the permissions are imported as well. It should work as is. But XenForo's default behavior would be to have users as primary members of Registered and then add Subscriber as a secondary group membership.
3) Those custom forum permissions should be preserved by the import so it should function the same way in XenForo. But it is good to carefully review the results.
4) Did you import twice into the same XenForo installation? That will create duplicate content.
As for your specific admin account which is duplicated... that is typical with an import. If both accounts (XenForo and the imported vB account) have the same username or email then the import program should flag them for a merge. Or you can manually merge them after the import:
Admin CP -> Users -> Search for users -> [find the user] -> Actions -> Merge with user
The merge will automatically associate all posts, private messages, etc.
XenForo might have its own definitions for some of the same smilie codes that vB used. You can modify XenForo's smilies:
Admin CP -> Content -> Smilies
Let me know if you have any other questions or problems. I have done a lot of vB imports.
XenForo Support Today at 2:02 AM
Imagine you have 10 different usergroups. And imagine you want all of them to "can view nodes", which means they can see the forum categories etc.
Now if it would be the single system, you would have to go to 10 different groups and give all of them the "view nodes" permission.
But the XF way is much better. Since everyone is in the registered group primaly, give this "can view nodes" permission and now all people who are in different 10 groups can view aswell.
Everytime you install an addon (which has a new permission), you would have to give the same permission to all of the groups again and again. Let's say you are unsatisfied with one permission, now you want to revoke it. Now you have to go over all of them again and revoke it. Do you see how tiresome this is?
So, the XF system is cummulative. Everyone, any user (admins, superadmins) etc. should be in the registered usergroup primaly.
Now you think about what ALL of these groups have in common. What do they share together? Probably "can view", "can post" etc. permission. So the commonly shared things, you give that to the registered usergroup. And anytime a new addon comes and implements a new permission like "view calendar, view Resource Manager", you go to registered and give it to it. 1-time and done. No need to go to 10 different groups.
Now, after you set up the common permissions for the registered. Now you can go individually to the other groups and give them their special permissions. Like for admins "can ban" or whatever.
About private nodes. That is easy. You go in ACP to the node and set it to private with a tick. That means now NOBODY can view that node any longer. Now you have to give specifically to each usergroup the "view" permission, just like you wanted in first place. This is a safe mechanism. Nobody ever can see a node accidentally, unless you specifically allowed them in the nodes settings.
HELP[ is available, but you still need to read between the lines and above all, read slowly. I'm close to reading in another import and slowly, but surely, I'm making sense out of this stuff and connecting the dots to our existing forum softwware.