hi mate i got this problem when putting mine on! i pressume its on the front that the most noise is heard?
my problem was i used the top and bottom nuts supplied with the coilovers, the bottom nut however that fits in the top mount on standed suspension is slotted, unlike the one supplied. (hence VW special tool, but i got an old piece of pipe and hacked it up to fit the shape)
if the garage have used the bottom nut supplied with the coilovers then it makes the clunking sound. this is because the slotted nut that should be used sits inside the top mount and and holds the coilover in the top mount bearing allowing it to move freely. the supplied nut sits ontop of the mount so the bearing is rendered useless and the clunking you hear is the top mount rubbing on the inside of the chassis.
Does it make this noise more when doing 3 point turns etc?
to check if they have fitted the right nut take the strut caps off the top off your suspension and if the top nut you you sits very high on the thread then they wont have used the slotted nut (it sits higher with the supplied nut because it sits ontop of the mount rather than inside).
i've got pictures of when i did mine i'm at work atm so i'll find them when i get back!
hope it helps and feel free to pm me if your stuck!