This is where you need an accountant. It's fine to look after these things yourself if you understand the principles, but if you don't (and most people don't) then I would strongly recommend you use an accountant to get your accounts setup. A good accountant would help you setup something like Xero, Freeagent or whatever so you can get up and running on your own accounts - showing you what to do on a monthly basis. Then when it comes to the year end their fees will be fair and they only need a quick tap and knock, and your accounts are filed at Companies House and HMRC with ease.
As a very general piece of advice, you actually won't have any pay for a while from your new company.
You put a loan into the company, lets say for easy math you invest £12,000 into the company as a loan. That gets recorded on your Balance Sheet as a debt the company owes, as mentioned earlier. As far as Companies House would be concerned, should you file your accounts with them in that time, it would be a debt.
You then take out of the company £1,000 a month to live on. This would not be wages, it would be the company paying you back £1k a month of that loan for 1 year.
As far as the tax is concerned there is no PAYE because you haven't had any pay from the company, you've earned nothing to put it another way. However the company has gradually been repaying it's loan to you - and you have been using those repayments to put food on the table and live on.
I'm perhaps oversimplifying it there, but that's a summary of a tax efficient way to invest into a company if any of that investment is needed to "pay" you too.
As for using an online company formation service to setup your company, almost all the ones you will find online are powered by the software my day job creates for that industry. I'm bias but our software is easier to use and less complicated that the Governments own platform and the cost between them all us comparable, even Quick Formations mentioned earlier that I sold in 2014 still runs on our eFiling platform. You're no better or worse of using a formation agent website or doing it on the gov.uk website yourself at a basic level, I just think the formation agents website would be easier to use.