Ufff! Its been a big pain in my ass. Fortunately (or maybe unfortunately) there have been enough people problems similar to mine that generally a google search would yield a solution. Here is a bit of what I went through. BY FAR, the most important thing you can do is save a copy of your old blogger template (that is, assuming you have modified it - if not, then chances are your upgrade will not be as painful as mine). You won't be able to use all of it, but you will be able to mine it for useful code here and there.
The first thing I wanted to do was to add a third column where I could place advertisements. Although creating a third column was not too difficult (its very similar to how you would do it on the old blogger - instructions here), populating it turned out to be a big pain. First, the GUI blogger builder obviously does not support the creation of new columns (no surprise there), so you need to edit the html. The problem is that the Beta Blogger either would not save my changes (when I tried to post an Amazon banner) or else the advertisement would not be displayed at all (when trying to display an Adsense banner). Although I've yet to figure out what is wrong with the Amazon banner, here is a useful post explaining how to get Adsense up and running the way you want.
Next, tried to tweak my profile using the GUI builder, but it has very limited functionality, so I ended up deleting my profile entirely. To really get what I want, I'll have to go and edit the code directly (note: much of the raw code is hidden in the normal Edit template mode, so make sure you "Expand Widget Templates" - this took me way to long to figure out, and I'm still not convinced everything is shone). For me, this is considerably more difficult than in the old blogger because the complexity of the code has increased drastically. Finally, I wanted to insert links to Digg and Del.ici.ous - and fortunately a quick internet search yielded exactly what I wanted. That's where I left off. I have the basic functionality I want, so now its all about tweaking it what I have