After adding E-junkie Cart buttons to my site, the cart itself looks messed up.

Because your cart appears as an overlay "inside" your own page, it is inheriting CSS from your page/site. You would need to determine how your own CSS is affecting the cart, so you could edit your CSS to fix that. To help you troubleshoot this, we can recommend using the View Source Chart extension for Firefox (and of course the Firebug and Web Developer extensions are always handy for advanced users).

Once you have the View Source Chart extension installed, view the cart in your page, right-click on it and select View Source Chart. You will find the cart added as a large DIV at the end of your original page source, so you can figure out how your CSS is getting applied to elements of the cart. You might consider just making exceptions for the cart by adding style rules for the div#EJEJC_window selector at the end of your CSS. E.g., if your site's CSS is making the cart appear all-black, you might do something like this to override that and make the cart background white again:

div#EJEJC_window {background-color:#FFF !important;}

Depending on your site's CSS, you may need to experiment with adding more specific CSS selectors for elements nested inside that main cart DIV, e.g.:

div#EJEJC_window,
div#EJEJC_window div,
div#EJEJC_window table,
div#EJEJC_window td
  {background-color:#FFF !important;}