aphex_guy: The flares are meant for blowing up the buildings marked on your map, as well as most of the stationary trucks. Bare in mind that the cannon is firing from the head train, so it might be obstructed in some cases.
Generally in this mission, the more noise you make, the more the rebel's attention will be on you. Best leave the majority of the gunfire between the soldiers and the rebels, they should keep each other busy so long as you stay quiet.
If you do have to fire off a few rounds, try moving to a new position afterwards, as the rebels will investigate the last spot they heard gunfire coming from. Knowing this, you can actually use it to your advantage to get the drop on them.
Also, as with most games, quicksave is your friend!
hope this helps, good luck.
I can get to the north target easy enough, I just can't seem to find a way of blowing up the trucks and the south target, do i need the demoman?