When I install fixed shelves in an open cabinet such as a bookcase, I often use use biscuits, but until I used this little trick, I had difficulty getting them aligned perfectly with the face frame rails.
Before assembling the case, I clamp the two sides together along the front edges, and using a framing square, mark each side where the top face of each shelf intersects. If one side is actually a partition, I do the same but allow for height differences.
I then unclamp those parts and clamp the first shelf, face down, on one of the sides, so that the top of the abutting edge of the shelf is aligned with the mark on the side, and the front edges are flush. Make sure the shelf is positioned so that it would “hinge” into its assembled position along the marked line.
Then mark the biscuit locations on the bottom face of the shelf, and cut the biscuits in the edge of the shelf with the joiner laying flat on the cabinet side, registering on the joiner bottom instead of on the adjustable fence (fence must be in the folded or stored position). Next stand the joiner up on end and align with the same marks, registering against the shelf edge, and cut the slots in the cabinet side.
To help understand how this works, you can put each shelf into position, tape it to the side along the top face, then fold it down flat to cut the slots, but this tends to be less accurate in practice.