Sanding between boards for smooth finish
If the difference isn't very great, you could sand them down with a belt sander. This is probably best if your wall is a bit uneven and you need a very slight taper.

Otherwise, you may want to use shims behind the thinner piece to make it flush at the surface. Then fill the edge of the slight void behind the beam or stile with caulk.

A third solution would be to plane them down, but this won't be able to account for a taper like the other two above methods.

Whatever you do, the most important thing would be to make sure the biscuit joints still line up correctly for the front side! So anything material you're removing should come from the back, if the uneven wall is the cause of misalignment.