They were certainly in service at the same time, so if you just want to have them on your layout at the same time that's no problem. As for having them running together, its possible but probably wasn't common. Santa Fe tended to keep the Fs in sets until near the end, but you could get away with it. Both warbonnet passenger Fs and blue & yellow freight Fs were used in freight service toward the end. The freight Fs would be more likely to run with SD45s but either could've possibly happened. The SD45 would be best in the early blue/yellow scheme as the blue/yellow warbonnet didn't appear until '73 and they probably weren't repainted quickly. It would've been theoretically possible for an F7 to run with a freight warbonnet SD45, but not as likely.
A picture at http://atsf.railfan.net/cowls/f45.html
shows a warbonnet F7b trailing 2 blue & yellow F45s, providing steam for heat on an Amtrak train, though the F45s had steam lines & high speed gearing to run with the FP45s on passenger trains if necessary; SD45s didn't. Also, on the Santa Fe, only F7Bs has steam generators, so Fs on passenger trains had to be in at least A-B sets.
GN's SDP45s (and SDP40s) were used with other power. See http://www.rrpicturearchives.net/showPi ... ?id=818239