Even with your cams lined up with the notches you will have some valves open. There isn't any given time where all of the valve are closed at once. You have looked at the TSRM link that's been given right? Is so, there shouldn't be any question as to how to set your timing. Can you take pics and post each step of what you are doing? That would help us help you.
BTW, as mentioned before we have a non-interference engine. Meaning, you can turn the crank while the head is bolted down and none of your pistons will touch the valves. Even when the valves are fully open. You will not bend a valve turning the crank to get the timing marks lined up correctly. It seems as though you are afraid to bend a valve doing so. No worries with our engines.