There is a pretty good tutorial over at Hit-or-Miss on combining two seperate blogs with two seperate templates into a single main index using MovableType. It's really easy to integrate, so if you looking to combine a "sidebar" style blog with your "regular" blog, you might take a look at it. It's fairly straightforward and should be something you can set up without too much trouble.
This tutorial is just a hint at what we did at Fanblogs to integrate eight blogs indexes into one index, with all the formatting in place, and eight blog RSS files into one combined RSS. It should also be noted that – even though I am doing a "Daily Links" posting that would seem similar – this is not the method I'm using.