I’ve never heard of a screenwriter having two agents – meaning different agents at different agencies. Typically larger agencies have offices in different cities and countries so if you’re with a big agency you essentially have representation in different countries through their other offices.
If I were you I would try and find a local agent first. While you don’t necessarily have to meet face to face with your agent it does help to establish a relationship. Once you have a local agent you can simply ask him/her if they think you should try and find representation in Los Angeles. I suspect most agents won’t want you do this but you won’t know until you ask them. And then at that point you can decide what’s best for your career.
Keep in mind when you’re submitting your material to agencies you don’t have to wait to hear “no” before you submit to the next agent on your list. So submit to as many as you can as quickly as you can and submit to ones in NYC and in LA while also submitting to local agents. When the dust settles if you’re lucky you’ll have a few choices and can find out at that point by asking the specific agents you’re dealing with if you can sign with more than one at the same time.
Make sure you read my post How do you get an agent for your screenplay? (And why you don’t need one!).
If you’re serious about screenwriting you should also think about moving to Los Angeles. I explain why in my post Do you have to live in Los Angeles to be a screenwriter?