If you buy a THROUGH ticket that involves cross London travel it will always include the underground. If you split the journey (unwise - usually more expensive) then it won't - but buying Selby to Waterloo, Waterloo to Basingstoke will get you a slight reduction on Selby - KX, KX-Waterloo, Waterloo-Basingstoke.
And don't use thetrainline - they charge booking fees
Use
http://www.eastcoast.co.uk/
They will have the same fares as thetrainline, charge no booking fee, and for some fares throw in an extra 10% discount