Help understanding user roles with WPMU

I have another thread related to this topic a little but have some other questions so wanted to see if I couldn't get them all in one place.

So, for a new WP guy I am learning the ins and outs of user roles and permissions but having some trouble here and there.

First, I have a multi site install and all users registering show up as users under the network admin panel only.

They do not show up as being a user on my main blog nor the second blog.

This is the part I was discussing in another thread and looking for clarification on. It seems like the users get added to my network but have no permissions on either of the sites. I have to add them before they can use my main site which truly is just incool. I am sure this can't be the way things are suppose to be so either I have a setting wrong or some other issue going on. If someone could maybe give myself and others the user role and process of registration for dummies version I would greatly appreciate it.

I do understand the role ladder and what each does it's the process from registration to actually being a subscriber on the main site I don't seem to have right.

The next part comes to the second blog/site. It's an arcade with lots of games and integrated properly so users click on the link to the arcade and are already logged in. I reviewed the settings and people can post comments if they are registered and logged in and no moderation is needed.
Not the case for my users as every comment made goes into moderation and I have to approve them before they get posted. The fact that they are not in the USER list for that site has to be the reason why they are not able to post comments. I can't believe I will have to also add all the user registering on my site to this second site just so they can post comments. Especially when they show up as being logged in on that site and all their arcade scores registered when they play the games.

I appreciate any and all help with getting this mapped out and fixed if changes are required on my side.
and

If it matters I am running all current versions of WPMU , Buddypress, BBpresss and do not have that I know of any specific plug ins managing users or their permissions.
Thank you.