As Ian mentions, to get the ultimate from your engine, your cam-timing should be set up with a 'degree-wheel'---there are a number of 'U-tube' films showing how to do this. However, for most "road-only use", a new timing chain and sprockets set fitted to the 'factory marks' will be perfectly sufficient. Yes, on a dyno you will see a difference in the power output, but on the road the difference might be difficult to discern. I would suggest that unless you are an experienced engine builder, for a "first time that I have buit one of these engines" effort (and for some people it will be THE first engine that they have ever built), keep it simple and go by the 'factory' marks--a 'dot' ON the tooth of one sprocket and a dot BETWEEN the teeth on the other. The cam sprocket will only fit in one position on the camshaft and the woodruf-key on the crank sprocket ensures that is in the correct position.
Fit the crank sprocket on first, then find where the cam-sprocket will align with the cam-shaft, then put the chain over the crank sprocket and then onto the cam-sprocket and then place the cam-sprocket onto the cam-shaft. It might not look like it will, but I assure you, the cam-sprocket holes will only align with the threaded holes on the camshaft drive flange in one position. Don't forget to use a new pair of tab-washers to lock the cam-sprocket screw-heads.