Had a Bit of a Scare Last Night for the New 6.0.2 Update

I am not sure if I can put this into words, but I plugged my iPhone into my MBP via the TB cable. I realized there wasan update so I updated the iPhone with it plugged into the MBP and iTunes. Once it was done and restarted, the update from iTunes which had registered as there being a newer update started to install the update again. I did not catch it until I saw the update bar on my iphone going through the updating process again. I had just done a backup via iCloud right before I plugged the iPhone into the MBP. this is where it gets confusing for me to explain what happened, it said that it needed to restore since there were some items on the iPhone that were purchased or newer than what the backup picked up. the iPhone finihsed with what it was doing and the slide bar on the iPhone had several languages on it, the screen was a black mesh type screen, but I did not slide the bar over to get to the home screen concerned I make things worse. I was not sure if I should unplug the iPhone from the MBP, but it got stuck at filling up the bar just below the apple on the iPhone. I waited and waited hoping it would finsih doing what it was doing. I had to eventuall disconnec the iPhone from the MBP and I tried to turn the machine off by the on/off button at the top. it did not do anything, so I plugged the iphone back in to the MBP and it showed in color a picture of the TB cable going up and a picture of the iTunes logo right above where the TB cable stopped. I was not sure what thi was telloing me. I did unplug it again, bit this time it had restarted but all of my icons for the apps I installed were gone. I plugged the iPhone back in (btw, the iPhobe was showing that it had the currenbt update of 6.0.2. I did a restore since it had just done one but it ws in the cloud and I was not sure if I plug the iPhone in if it would automatically resotre the iphone from the cloud since I had never backed up to the MPB. it did restore the icons for the apps I put on the iPhone, and it seemed OK. For some reason it downloaded all the 256 songs again fromi/tunes even know I have just the songs I want on the iPhobne checked. I am not sure if the setting were all reset to the factory settings and I am not sure how to tell, It did make my iCloud email account as my primary account when before this all happened I had my gmail account as my primary account.

anything that I should do to check and see if the iphone is set up right? I never really did learn how to use the Settings correctly, so I am not sure if they are set up right. I realize this is not the best description of what happened, but I do not want to go through this again. My itunes picks up that my iPhonein close by when I open itunes now, and I guess one of the recent updates makes it so that you do not have to have the iPhone plugged in to download and install the latest iPhone update. Is there a way to check to see if I somehow damaged the iPhone? any suggestions?

thanks