Trying to understand what you did here. So, if you did it "freehand" by which I mean largely by making your own marks on pulleys belt and engine casings, then at the bottom, you made marks on the crankshaft pulley, timing belt and engine casing? then did the same at the top with the camshaft pulley, timing belt and engine casing? Removed the old belt, copied the cam belt marks over to the new belt and then fitted the new belt with all marks lining up? You talk about the marks not lining up after two turns of the engine? This is two revolutions of the crankshaft which equates to one revolution of the camshaft. If everything is fitted correctly, after turning the crankshaft two complete revolutions you should find that the can pully mark should be lining up with the mark you made on the head and the crankshaft will, of course, be lined up with the mark you made on the oil pump casing. Any marks made on the timing belt will NOT line up with the pulleys however.
Alternatively, if you didn't do it "freehand" - So if you used a locking tool kit but didn't slacken the camshaft pulley bolt (which is how I like to do them) I suspect that what you may have done is lock up the crankshaft with the locking tool and camshaft with the locking bar and then tried to fit the new belt with both of these tools still fitted? It's impossible to do this unless you either slacken the camshaft centre bolt on the pulley OR, if not slackening that bolt, remove the cam locking bar and turn the cam pulley clockwise by about half a tooth which will now give enough slack to engage the belt teeth with the cam pulley.. When you then tension the belt tensioner you'll see the cam pulley turn slightly anticlockwise thus letting the slot in the camshaft line up so the locking bar can be inserted - all the time you're doing this the crankshaft will be locked.
No matter which of these methods you used, Marks made on the cam belt will not subsequently align with the pulleys after doing the two revolutions to check the engine is free.
Hope that helps?