You can't really do the standard SHOW S01E01 thing one would normally do with TV shows, because classic Who was told in serials for the most part, like each "season" of classic Who was more literally just the year of production in most cases (it seems most fans would rather pretend The Trial of a Time Lord never happened...)
What I mean is that if I were to structure episodes of classic Who the normal way, it would be kind of confusing and vague. CDW S12E06 doesn't really tell you that it's Part Two of Ark in Space, which was the second serial of that season.
The only, clunky sort of way I can think of would be to do two S's, one for Season, the other for Serial/Story. So CDW S12E06 would become CDW S12 S2E02 or something...