Transferring apps to new iPhone after it was partially set up at store?

[iMore Question]

My husband went and upgraded both of our iPhones. He took my old phone with him to the store and returned home with both my old and new phone. The store only partially set up my new phone. My new phone only has my contacts, photos and email. No apps or music was transfered. The apps are important because a few of them contain lots of data, such as anotes, mapmyfitness, a step counter app, and a paid for calander app, and a measurement app that I use frequently. To make things more confusing, we had a line on our account that we were paying for with no phone attached to it, so he attached it to my old phone. Now my old phone has a new number. I'm lost on how to transfer everything at this point. If I sync my old phone to iTunes, will it still sync to my new phone (considering my old phone has an active number attached to it)? What do I do? Thanks in advance for your help.