One thing I have done is to clamp a few of the pieces on top of each other and line them up so the 45 degree side continues from the lower piece to the top piece effectively doubling the thickness of the surface. Now get down next to the pieces with the fence loose and holding the fence knob with one hand let the domino conform to the stock angle so you cannot see any light between the fence and the stock then carefully clamp at that angle. Now if you make your domino mortices at even intervals from both ends you can mark both pieces at the same time(or all 4 if you can stack them all at the same time).
The key for getting good mortises on an angle is in the presentation of the Dominoe to the stock. You have to make sure the base of the fence is tight to the stock when you plunge or it will mortice more towards the outside of the beveled cut I always have several clamps on the stock, then I use my clamping hand to hold the fence knob down and if I can wrap my fingers around the back side of the stock for extra clamping. I used to plunge the Domino with my hand back by the plug, but I have found it better for me to hold the Domino with my thumb and forefinger right where the Domino gets thinner on the body.
Anyways, maybe more info than you needed? Hopefully it helps.