So I am going with an entirely fluid layout, using only pixels for min-max values. I am not sure about the use of em vs. percentages, and how they relate to scaling. Currently, I am using em for margins, font sizes, and general spacing issues. I am using percentages for the width of the divs. So, is there a 'best practice' on what I should be doing about this. Should I use all em or all percents? If anyone could point to an article or two that deals with this it would be appreciated. Thanks!
In my opinion you're got it right. Use percentages for width of elements, em for margins, padding, font sizes etc.
You may want to use css media selectors to create multiple fixed size layouts depending on available area, a good example of this is available at getskeleton.com Ultimately, it's all a matter of personal preference, the various units in CSS are just tools to do the job at hand - just remember to keep usability, cross browser functionality, and accessibility at the top of your consideration list, and you'll be fine.
px is best for fixed layouts % and em is best for fluid layouts But yes yo have got the concept down pat. Just make sure you keep padding and margining in mind. Fluid layouts cause for a little bit of math or good ol trial and error.