Don't do it yourself unless you are an accountant. Its a waste of time for you as an entrepreneur. (there is too much to figure out) Hire a local accountant in your area, who you can call on the phone, and submit your yearly's.
That's the premium and only solution for someone who wants to focus on their business, and keep things 100% right.
The way I do my accounts, is I have a years spreadsheet, the date, and description, and debit or credit amount, and reference number, and vat. And I just at the end of the year, go back through my bank statement CSV, and match up my "business diary" spreadsheet, with that's in my bank account statement. Once they match and I know I have all the invoices, I send the diary to accountant who produces the goods, and submits them on my behalf. There are also a couple of things like admin type forms I have to fill in, these seem to be updated and change every year, so I just fill them in when my accountant sends me them. They are the ones with the knowledge.