Is it possible to track only selected episodes from seasons with shows?

Worst case you could make a list. But I believe what you are looking for is an alternate order…

Details on how to use:

http://forums.trakt.tv/t/support-for-alternative-ordering-of-episodes-aka-flexible-seasons/3832/14?u=arcreactor

The X-files:
https://trakt.tv/shows/the-x-files/seasons/alternate/776#

Hope this helps!