I have both as well, the 8" with the longer sight radius is going to be easier to aim accurately, but I don't think it is more inherently accurate. As far as as government contracts, during the WTBS, 8" would be period correct, however the idea to shorten barrels on C&B revolvers is not a new or novel idea, and individuals in the period also saw the possibilities and there were examples of shortened barrels particularly after the war, but they were not official issue.
Then again, the stainless, accurized and target 8" models of the 1858 available now, that help to get the most out of the pistol, are not any more period correct than the 5.5" barreled version, adn when you really get right down to it, none of the current replicas are exactly period correct, it is simple a matter of where you set the goalposts for the "most accurate" copy.
The shorter model is handier, and easier to carry in a holster, and it is near certainty some enterprising young men cut the barrel of their Remingtons in the late 1800's. It is harder to shoot the shorter model well, mostly due to sight radius, but the weight in the front does help to steady the sight picture as well.
If you are going to b e reenacting with particular groups, then an 8" will have to do, if not then if you have the chance as with buying any handgun, try handling both, and if possible shooting both and decide which fits and feels better for you.
An alternative may be the "Navy" .36 model which has a barrel length somewhat in between the two and handles a bit differently than either.