Simple, just start from the first Brotherhood mission and work your way through them. There aren't that many to do and as far as I am aware you needn't do every stronghold although some may require you to do before you can advance.
Just bring up your map, find a brotherhood icon and go do it - working with a co-op friend is also advisable as it not only makes it easier, but you can work towards the 'Separated at Birth' achievement too.
Use this website to locate all of the missions and strongholds:
Map no longer available, sorry.