I'm currently doing exactly the same thing here in the UK, with Harlequin 3mm floor. The best way we've found is to have the floor running US/DS, rather than SL/SR - we then keep the excess floor on the roll and hide it upstage of the cyc. We use the back of the prosc as our setting line, and start laying out from centre. This means that a) we can have excess in the wings, b) the marks are all in the right place, with the same relationships to each other, and c) any excess floor is hidden from view.
As we're near the start of our tour, we're doing a run of one of the pieces in each venue, but when we get further in, having class onstage, and allowing the dancers to work steps out themselves will be sufficient!
Hope this helps with your problem.
C