I assume you wanna change the color of your outgoing bubbles? Cause the incoming bubble color can be changed at the Adium's preferences. But the other color can be found in main.css inside the Adium Matte.AdiumMessageStyle, just edit this part of the file:
.msgContainer, .msgContainerContext {
background: #b1e14f url("images/TopLeft.png") top left no-repeat;
position: relative;
min-height: 15px;
}
where of course '#b1e14f' is the part you wanna replace with the color you desire.

The incoming bubbles also have their own css-style files in /Contents/Resources/Variants, just open one up and edit it the same way just mentioned above.

I hope this helped.

Now you don't have to, just install this one ;)