Content Type vs Webform vs Form API vs Custom Form vs?
I'm using Drupal for exactly the same purpose. Basically, what I'm doing is using the Field Group module to wrap particular items together in DIV tags so that I can use CSS styles to properly layout my forms.

Drupal provides a very structured set of container elements with appropriately named classes. Accordingly, leveraging the power of CSS to your advantage should be the first thought that goes through your mind when it comes to manipulating layouts.

I mucked with the Webform module, and although it is quite capable, I've found that just sticking with Drupal's standard content type system for collecting information has suited me best.  Utilizing Views and the Rules module, I'm able to generate reporting pages that show me the critical information I want with less modular bloat to my Drupal installation.

So definitely read up on Views, Field Group, and the Rules module to see if the functionality as described will fit your bill.