Not quite clear what you mean.
You can only earn miles in one programme - so you can't earn miles for the underlying economy seat in one programme, and the "upgrade" in a second. (i.e. you can't earn two sets of miles - one for "P" and one for "C")
If you have already associated a frequent flyer number (whether for TK's programme or any other *A programme) with the ticket, then the miles for your ticket will end up there.
If you have already associated a frequent flyer number with the ticket, but now wish to change it so the miles end up in TK Miles & Smiles, then this may not work out well.