Login of Alfresco users into Joomla! isn't supported yet by the official integration. Based on the feedback we have received this is a much wanted feature and we have it high on our own wishlist for version 1.1. Joosco does indeed not use CMIS like our intergration does, I haven't looked at their code yet but I can imagine that their plugin can be used in tandem with our code. Or if you don't like to fiddle with code you could wait for the next version of the official integration.
The integration can make full use of template overrides so you can completely customize it your needs. I did design it using milkyway to suit the default style of a out of the box 1.5 but adapting it to your needs shouldn't be that hard.