Have you read their getting started material? If not, it may help:
http://www.youneedabudget.com/method
(The 4 'rules' are what I'm talking about)
Basically, what you do is first, input the initial balance on all your accounts - that includes checking, savings, credit cards, etc.
Then, tweak your budget categories if you want. The default set they give you is good, but you may want to change or add some things.
Initially, unless you've been keeping a budget for the past while, you'll guess as to how much to allocate to each budget item.
Your goal, if possible, is to
budget all of your expenditures for the month based only on the money you already have in your accounts. You want to create a zero-based budget, where the budget number at the top of the screen for the month is neither red nor green: if you have money left over, put it somewhere (e.g. savings). If you're short on money, cut somewhere.
As you get income, you'll be able to allocate more money in your budget. Ideally, in the YNAB system, you'll want to record all of your income as counting towards next month's spending. If you can't do that now, that's okay - but that's the goal.
Other than that, sounds like you're on the right track! The YNAB community forums are actually pretty good too, if you get stuck. I had some questions about how to handle certain things in the set up, and I found the answers just by searching the questions that had already been asked. Good luck!
