The Allez is Specialized's introductory level aluminium road race bike, with a race geometry. This means that you are bent over reasonably low on the bike and the bike is very responsive.
The Secteur is an aluminium version of Specialized's carbon fibre Roubaix range, which is designed for comfort over longer distances, but still gets you there quickly. It has a more relaxed geometry, as per Ianrauk's comment and a fractionally longer wheel base. This means you sit slightly more upright and there is a more relaxed feel to the handling than you get with an out and out race bike.
Which one is better? I would suggest getting down to your local bike shop (LBS) and taking both for a test ride, rather than ordering over internet without testing. Bikes are a personal thing and you will know which you prefer. That will be the right one for you.
Hope that helps