First things first, your attorney had no choice but to include all of the credit card debt. Not including a debt in your Chapter 13 filing is known as showing "preference" to one of your creditors and it is illegal and can cause serious problems in a bankruptcy case.
As far as reaffirming your secured debts tied to property you did not surrender in the bankruptcy, this isn't usually a matter of choice. Some states require reaffirmation agreements and some do not. If yours does, then you reaffirm or run the risk of losing your car/house/whatever. In a Chapter 13, reaffirmation agreements usually are not required as your Chapter 13 plan and Schedule J should show the creditor that you can afford to and intend to keep the property (which is ultimately the purpose of a reaffirmation agreement - that and to protect the creditor in the event of default).
I do not know that you scores would increase as a result of reaffirmation. Unless the creditor stopped reporting when you filed your Chapter 13, it shouldn't change anything.
Using credit at all during the life of a Chapter 13 is generally not a great idea, but if you are going to it will almost certainly need to be using a secured credit card. Getting a mortgage is damn near impossible while in a Chapter 13, so I wouldn't hold out much hope of that happening until your discharge and you start rebuilding.
