only last week i was faced with the same problem and the answer is... with difficulty! and much due care, patience and painstaking work! but it can be done.
scribe and fit the two sides first then rout out the female joints. put the worktop that forms the end/bottom of the 'U' in place and draw (use masking tape on the 'face up' male joint end of the worktop.) the outline of the cuts. you will find a couple of offcuts of the worktop are useful here to pack up the worktops where required.
then, carefully draw another line at the correct distance away from this one, to allow for the guide bush on the router (usually 9mm or thereabouts, check to see if it says in your manaul for the jig or guide bush). now carefully align your jig to this and away you go! would love to know how you get on.
just a few top tips.. always cut left to right!,
if your working with high gloss black work top mark with a stanley knife to get a clean perfect line to work from,
use a peice of card between the clamps and worktop surface,
make sure the clamps you use are g-clamps and once tightened dont allow for any movement,
when cutting the butt scribes go through first only bout two mill or so and then follow with a jigsaw (very important when cutting worktop face down!, also helps with the life of the blade). 8)