Whether you are melting-in a C/Steel base metal or a C/Steel filler material, there should be no difference from a compositional point of view, because you are melting both, which then mix into the weld pool. As such, there should be no "compatibility" problems relating to the filler compositions.
There are however potential problems with welding a non-fluxing process (e.g. GTAW, GMAW) over a deposit from a fluxing process. (e.g. SMAW, FCAW) This happens because there is always SOME of the flux from the fluxing process around. Non-fluxing processes are unable to handle this flux, and can lead to porosity or lack of fusion.
As a general rule then, you always first deposit the non-fluxing process and then the fluxing process.
Hope this helps
Regards
Niekie Jooste