Cercanías train are included (reddish c-sign), metro not (diamond shaped sign).

C-2 and C-7 are cercanías. If you have a continuous pass or an already active travel day, you can indeed use it to travel on these. On gated stations, you'll have to ask staff to open the access gates - if there's no staff present use the intercom buttons. It's a bit tedious, and some staff don't seem to trust it, but it's the only way. I've also encountered broken intercoms (if that happens: all ticket machines also have one and through that one they could also remotely open the access doors)

If you have a reservation for a long distance service booked at a Renfe ticket office, you can also use the "CombinadoCercanías" (free Cercanías before/after a trip on a long distance train, should be mentioned in the second text row on the ticket) barcode to open the access gates from 4 hours before departure of the long distance train.

If you have a flexi pass and no travel plans outside Madrid for the day, I'd say it's not worth using a travel day - Cercanías is relatively cheap. You can even get the temporarily free subscription (€10 deposit that you'll get back if you use it more than 16 times - at least until december 31st 2022). It has been announced that the free Cercanías subscriptions will be extended from January to December 2023, but the exact conditions have not been announced yet. 

You cannot use it on the metro, so unfortunately not on metro line 9.

Greetings from Madrid!

Thanks for that. As you can’t seem to get a journey between these stations on the Rail Planner App and add to the pass, do you just show the station attendant the global pass scan code or do you need to manually add the start/end stations to the my journey part of the App.

Officially you need to (manually) add all the journeys. 

Indeed. It's a pain for for the Cercanías, just because RENFE don't find it necessary to disclose their Cercanías timetables to the rest of the world :(

On several such lines in MAD the service is so intense and varies per day, that there is not official timetable at all-it just says like ´cada 4/5/6 minutos.. or the like. C is always Cercanias=RENFE, some lines go quite far out of town till like Guadalajara (but not in MEX), some 50/55 Kms away.

IF you look very thoroughly in some larger estaciones there will be some poster hanging out-perhaps even still legible, which has the orarios on it. Mostly useful for very first/last trenes of the dia.

In the Barca area with Catalan it was till very recently still possible with persistence and luck to get those small printed orarios from customerservice-though they guarded them like diamonds. Never seen that in MAD.

There is an official timetable. You can look it up. RENFE just do not share it a lot.