I've been under the impression that if you're self-employed, you only have to pay NI if you make over a certain amount of money.
This is true, but the threashold is something like ?6k a year and it doesn't sound like that's what you're dealing with. (Also, you should still file tax returns and make a claim for not having to pay NI.)
You can pay Class II NIC monthly by direct debit, but if you don't it would have been billed quarterly from when you became self-employed. (As of this month the bills come every January and July instead.) You're supposed to pay each bill within 30 days, so you're in arrears and may be fined if you tell them about it. However, I've paid maybe 1 in 3 of my bills on time, generally leaving the arrears to build up for up to a year and then paying it all at once, and I never got fined for that. If you register now and say you're ready to pay it all there's a good chance you won't have to pay any extra.
For Income Tax and Class IV NIC, if you started work before 06/04/2010 you should have submitted a tax return by the end of January (just for the stuff up to the previous April) and then paid whatever tax and NIC were due. If you weren't earning anything the rest of the tax year than it's likely that you were under the threashold anyway so probably fine. If you earned more than about ?6k that year then you owe tax, but you're not horribly late in paying it so it's not going to be a disaster if you declare it. Anything you've earned since the 06/04/2010 doesn't need to be declared yet and you have plenty of time to sort it out.
So, get on to HMRC and register now. If you just worked for a couple of weeks before the start of the last tax year I'd be tempted to leave it out to simplify things, but I'm not advising you do that, think it through yourself. You can get everything sorted out and it won't really be painful. Do start saving well for your first proper tax bill though (you're a year behind with the saving), or that'll hurt.