You don't need to use Trail Boss. If you are trying to develop a load that will work in the pistol and the rifle, the pistol is the limiting factor. I don't know where you got your 6.9 grain load data from, but it doesn't show on the current Alliant website. If you have that load from a reliable source, and it chronographs around 800-850 fps, you are probably good to go for using that load in the pistol and the same in the rifle.
However, you said it was a Ruger Peacekeeper, which doesn't exist as far as I know. If it is a New Vaquero, then you need to keep your loads within the loading manual limits for .45 Colt (and not for the much stronger Ruger Blackhawk).
In my Ruger New Vaquero I find that 6 grain Red Dot with 250 grain bullet is sufficient. A better load for CAS is a 200 grain bullet with 5 grains of Bullseye. Green Dot will work, but I have no experience or load data for it.
Nothing complicated.
Hmmm, well I don't have a Chronograph, but I do have the 49th ed Lyman book. That's where I got the greendot load, it maxes at 7gr, so I stay a 6.9.
Hey, could I just check the pistol loads there and cross-ref with the rifle loads to make sure it's not over the top? is that sensical?
And yes, it is a Vaquero.