As far as registering your business – Google Small Business Formation Structure. There will be numerous results, but they are all similar.
Here is the short version - You will want liability protection so you want to be either an LLC or a Corporation, meaning you will have to register with your Secretary of State, and the IRS. Your secretary of state, or city/county web sites, will probably have small business startup information also. At the Federal level you simply apply for an EIN online (the number is returned in seconds), and then start paying estimated taxes throughout the year. If you go with LLC, I should tell you that LLC is a state-recognized designation, not Federal. At the Federal level a husband/wife LLC is a Partership, so that is what kind of return you will file. If you are copyrighting or trademarking anything, that will happen at the Federal level also. At the local level there will likely be permits to deal with, once you have yourself established as a business entity. If there is insurance required, that will probably need to preceed the permit applications.
Once you are registered and have your EIN, take your registration papers to where you do your personal banking and establish a business bank account. Do not run your business out of your personal account, or you risk IRS trouble! I don't recommend establishing your business account with another institution, as it is somewhat difficult to move money across institutions to your personal account, or back the other way if you need to reinvest later.
If you will have an online presence, buy your domain name through either a registrar or the company you will host with.
Writing payroll checks – Quickbooks has a payroll service which you can subscribe to that will integrate with their package. It will do the calculations for you. I’m not particularly a Quickbooks fan- I have gotten Peachtree and although I haven’t used it, it seems more intuitive to me.
Quarterly taxes – there is a calculation form from the IRS. I find it very taxing (!), but at heart it calculates the prorated taxes based on your current earnings times projected end of year tax rate.
Assuming you are using cash basis accounting you deduct your out of pocket expenses as they happen. This happens on your business return, then the proceeds flow to your personal return. If you use accrual accounting, things get more complicated and you will probably want an accountant, but otherwise you can do most if not all of your bookkeeping without one.