I've just gone through the same process and found that the Jigoshop plugin for WP is the easiest to manipulate. I tried all of the others (Dukapress, Cartpress, WP-E-Commerce) and they either had a poor interface or were very hard to adjust.
With Jigoshop, get ready to use
display:none; a lot! I've found that the functions on the page were quite tricky to move around but most we're pretty easy to just hide via CSS.
Also, it has some very useful widgets. I've put together a little hack to display widgets where ever you want on the page so just let me know if you need some help on that.
The only downside to it is that it has very few payment providers integrated, this wasn't a problem for us as we're using Paypal anyway.