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Hi,
I had a visit from HMRC a month ago and it turned out that I should not have reclaimed for some purchase invoices in 2011 (previous financial year for my company, so not possible to correct through maintenance).

I have to submit a quarterly return in February and I'm supposed to pay back £250 of vat. Is it enough if I just post a manual adjustment (to account 2204) or is there a proper way of doing it, ie. post a journal to credit Purchase Tax Control account and debit the relevant overhead accounts (where originally invoices should have posted as gross rather than net)?

Yes...

You could alternatively enter a VAT only Credit note to reverse the VAT on the original invoice and then post a gross invoice to put it to the nominal. The invoice and credit note cancel each other off. you could also do it with a bank payment and receipt, but if it relates to a specific invoice on a specific account, then this is neat as it leaves a trail that shows it being paid and makes sure they don't ask for it again by accident in future.