Its not exactly that. The question is if you have service tax code, system will automatically create line items and whatever you have maintained in TDS will thereafter will get calculated automatically ,depending on the settings you have maintained in TDS tax type.
However if your very service tax is manual wherein you are creating the line item by yourself then obviously you have to do the rest of the things (The tds part) manually. System will not be able to make out the base amount and therefore will pick up whatever you have put in header amount field.
best regds
Subha