Em is generally known as the most effective font unit in CSS content development, because it is relative to the body text size of the page. So, each of your elements is sized relatively according to your current font size. Adding these units to margin and heights of divs will allow a proportional sizing, again according to the text size. In extend, this method will promote accessibility in your page.
A pixel unit on the other hand, is a pixel unit. It is easy to use and remain constant in value, regardless of your body text size. It does require some accurate calculations though (which does make it a bit of pain sometimes). Not to mention that not all users see it the same way. There are many articles online regarding the advantages of em and disadvantages of using pixel units.
Now, the question is how do I proceed to changing my pixel units to relative em units? There’s a great article at clagnut’s blog that will guide you through this process. Again, if you’re new to this (like I am), it can be painful and you might just feel like going back to pixels, since it is much more familiar.
Or, you can just get an online em calculator that will calculate your pixels to em units. I think the most know is Riddle’s Em Calculator.
Recently, I’ve come accross James Whittaker’s calculator that also provides the line height of your text. It gives you the full CSS rule for your element, ready to copy and paste on your stylesheet. You can check it out here. You can also install on your hard drive and have easier access on it. I love it!