I initially started my son on the 2 - 6 week routine (might have the weeks wrong) and when he didn't sleep the time allocated I just adjusted the times. He stayed on this rutine for months. So if he was to have up time for an hour well I'd start that after the 40 min sleep. My son used to only sleep for an hour and half or an hour. So I'd get him up, feed, up time (what ever was allocated for it on the routine) then sleep etc.
You do have to be flexible, especially if he won't resettle after the 40mins. Just stick to the routine an adjust times accordingly. I also used to wake my son if he was going to sleep past the feed times.
Hope this makes sense and helps.
Bett, NSW, 2 boys & Twins 19.2.08