Stuart
As you are an accountant by training, if i remember correctly there should be nothing much to worry about. Just sit them down with a cup of tea and give them the records they request.(Normally look at three years including vat returns, bank statements, up to date accounts and records)
They will have standard thing they look for such as ensuring that invoices and receipts have a vat number on them, expenses are another favourite especially if you are claiming fuel(they will check to ensure that the fuel scale charges have been applied).
They will of course also do a systems check to ensure that your record keeping is good(this means less work and checking for them), will talk to you generally about the business and have a look at stock on the premises.
At the end of the visit they should advise you of any under/over payments they believe you have made and any actions they believe you need to take.
Following the visit they should write to you outlining the outcomes of the visit and if any adjustment is required will issue you with an assessment bill.
All in all it should not be a problem and should only take about 3/4hours.