Before now, and to allow them to appear on the same diagram I have added in logical relatives with names such as XXXX, so in your case (if you know no more) I might add an XXX Ratcliff identified as the theoretical father of William and John. I know this is rather dodgy (and the may be cousins) but I had a similar issue as yours and could find no other solution.
Advice from the more experienced users of this forum will no doubt follow!
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