I know this might sound really stupid, but I'll ask anyway. Say I have a Charmander, and I breed it with a Ditto; I get an egg and take both Pokemon from daycare. I then decide to breed the same Ditto with a Chikorita. Will I still get any eggs even if Ditto is with a different partner?
Yes they can
Most people use Ditto to IV breed or Masuda Methoding to get shinys. Here is an Example:
I IV breed to get a 5IV Hoppip. First I Breed with a 6IV ditto on a Hoppip and Hoppip gets 3IVs all the time.. Then I breed it again on a Pikachu and it gets the other 3IVs that Hoppip needs now just breed them together and Ta-Daa. Ditto breeded 2times and it works.
Source and Breeding Myself
Ditto can breed with ANY Pokemon that aren't in Undiscovered Egg Group
Yes of course any Pokemon can. It may seem horrible but Pokemon don't have Pokemon rights.
Of course it can. ditto can breed with ANYTHING except legendary or mythical