Set up new iphone as new or restore to backup

I just purchased my new iphone4 today. At the store they transferred over all my contacts and got my email set up. When I came home I immediately backed up my old iphone and then proceeded to plug in my iphone4. When prompted I selected to restore to backup instead of set up as new phone. After I did that I began thinking that was not what I should have done. The folder that was combined on the iphone4 when I was at the store was no longer there (I know I can combine apps, but I am not sure how they were set up before). Plus now the email looks different than it did also, it looks just like my previous iphone did and when I was in the store it listed the mailboxes as "Yahoo" or "Gmail" not by the email addresses. So now I am thinking what else am I missing? Are there new ringtones or wallpapers that I am now missing?
How can I get my email to go back to what the iphone4 should look like?
Should I restore and then start over by setting it up as a new phone this time? Will I have to go to the at&t store to have them transfer my contacts again (I do not have outlook)?
I just wanted to ask for some advice before I go restoring things if I am not missing anything or if there is an easier way to fix it.