no! multithread. you always want to create competition for your deal. it is very likely some sources of funding will say no, and the way to get good terms from the others is to have multiple offers. YC is slightly different, in that the terms are set, but still.
I can't speak to YC specifically, but one normally would want to contact many investors in parallel. The chance of receiving funding from any one investor is incredibly low. If you contact them serially, you'll spend a hopelessly long amount of time raising money. Likewise, if multiple investors are interested in your company, they may jointly invest, which is somewhat common. Plus, you can use the competition to establish the fair market price of your stock.
I don't understand what you mean by YC protocol. Are you asking what we advise startups we've funded to do when approaching investors for further funding?