What to you use atm? I use Sage instant accounts.
It really depends on your accounts, how tidy, format you'd send to accountant, etc.
I used to input all my data onto excel spreadsheets, I took them to an accountant who kindly said he couldn't save me any money and if I found SA easy to continue to do it myself. He would have charged £300 to £500 but I'm not VAT registered.
I think you fill in returns quarterly?