I mark each board w/ which surface of the enclosure it is (top, bottom, left, right, front, back). I generally do this during a dry fit before biscuiting. Each marking is oriented so that it will read normally when the enclosure is standing upright and facing me (i.e. the marking for the bottom panel is on the inside surface with the bottom of the marking closest to the front panel).
I mark biscuit locations by holding the two boards in proper alignment and drawing a set of lines across the seam. If you want to be fancy, slant the lines such that they taper inward at one end. Since I do this by hand w/o measuring, the lines are _very_ unlikely to line up with any other board.
I haven't built anything that required precise alignment of internal braces yet. I'll be starting a 12" sub when I get back from vacation that will need this. I plan to mark the braces with numbers in order from front to back of enclosure. Since the braces will meet the side panels at 90 degrees in the middle of the panel (forming a T), I'll need to make reference lines that follow one side of the brace in addition to the biscuit lines. That way, I can position the biscuit cutter along the reference line and keep them all in a straight line.