It's easier to cut the corners (extended portion) of the cabinets, and install your quarter round. Just be very careful to make the cuts exactly the same height as the quarter round.
Use a scrap piece of Q-round to hold up to the cabinet corner, and mark.
May be easiest to use a sharp utility knife for the cutting.
How do I cut quarter round thinner in certain places to go around the vertical moldings on the corners and other areas of my kitchen cabinets?
ther are a few ways of doing what you want 1 you can rip something the same thickness of the verticals if you had any fillers left over 2 you could mark the cabinet and cut with a coping saw 3 you could notch the quarter round I would rip the filler hope this helps Rob