You should be ok if your running a single organization and don't need to take advantage of any of the features of the CRM 4.0 endpoint. The 2006 endpoint is for compatiblity with CRM3, while the new endpoint has all the features for CRM 4.0.
If you ever need to access the multi-tenant capabitlities of CRM 4.0 you can't do that on the 2006 endpoint as it only works with the default org.