1) I don't know what cIOS that guide leaves you with so it's kind of hard to answer. Seeing as how you followed one of our guides I'm sure you are good. Everybody seems to set their cIOS up differently based on what they need or want. For example some people still have Wanin's rev 17 in at least one slot but I don't see a point in it so all of the slots I used for Wanin's are rev 21 but with different bases. Same as people are still using Hermes v4 while I only have v5.1. The choice is yours.
2) Well you can make sure your IOS and system menu are up to date via online update but that defeats the purpose of softmodding. LOL.
Not really. There is PimpMyWii which is more likely to screw your system up than properly update for you so don't use it. DOP-Mii is good for updating your IOS but be careful with it and pay attention to what you are doing while using it because you can screw up your system. cIOS you just kind of choose to install as released.