One way - in your own forms - is to override CheckBlockingConditions, something like this:

Protected Overrides Sub CheckBlockingConditions()
  MyBase.CheckBlockingConditions()
  'check for DD tables
  Dim oDirectDebitSettings As New DirectDebitSettings
  Try
    oDirectDebitSetting = oDirectDebitSettings.First
  Catch ex As Sage.ObjectStore.InvalidObjectException
    Throw New Sage.Accounting.Exceptions.SageAccountingException("Direct Debit settings not present")
  End Try
End Sub

in this example, if the DirectDebitSettings custom table doesn't exist, a SageAccountingException is thrown, which prevents the form from loading.

If customising Sage forms, do a similar Try/Catch and set a flag to indicate whether the customisation code should be run.