Freeagent is book-keeping software, not accounts production software.
Companies House filings need to be in the prescribed format and not only that, but need to comply with accounting standards, so you have to adjust for items such as accruals, prepayments, depreciation, provisions, stock movements, etc., etc.
There are also occasions where the FAC tax provisions need adjustments.
Unless you understand accounting standards and what needs to be adjusted for, there is no "magic" software that will make FAC compliant for companies house purposes.