using Drupal as your CMS you are better off using the e-Commerce or Ubercart modules. Those modules were made for Drupal. These are exciting times for Ubercart and the e-Commerce module.
Drupal ecommerce solution faces with two choices, Ubercart and the e-Commerce modules, e-commerce is only compatible with the Drupal 5.x branch (the version for the 6.x branch is still in development). Ubercart has a version compatible with the Drupal 6.x branch (a beta version but already pretty stable) and the Ubercart community is very active.
Here are the Pros and Cons of drupal e-Commerce and Ubercart modules:
E-Commerce
Pros Cons
Endlessly extensible UI is difficult and confusing
More options for contributed modules Requires a lot of theming
Been around the block longer Feels bloated and cumbersome
Ubercart
Pros Cons
More ready to go out of the box Difficult to customize some areas
Lots of jQuery built in Lots of jQuery built in
Vibrant, active community Still in alpha
User interface is awesome Not as many modules available
As conclusion, there may be no solid answer for which one is better. However, there are a few things Ubercart offers that e-Commerce does not. Most importantly, is a one page checkout. Ubercart has a really nicely done one page checkout, while e-Commerce's leaves much to be desired. If nothing else, perhaps having them both will give us two strong options for using e-commerce in Drupal.
