Saying no is what the safeword "yellow" or "amber" is for. As in, "this isn't an emergency, but it's not working for me."
As for expressing a preference, my late slave-wife would have said things like "It'd be horrible if you twisted those clamps as well as pull them," or "I couldn't bear it if you used the cane instead of the flogger" - what we called "briar-patch suggestions," as in "don't throw me in the..."