Designing website from scratch and adding e commerce functionality?

[Ka]

Ok, so I have been doing a lot of searching and am not finding any clear answers. I am trying to build my small online business (online store), I got my products (some wholesale, some made from home). I can make a website and have no problems designing websites. My question is, can I simply make a website and add shopping cart functionality to it, I seen paypal has this option but there are so many companies out there that offer the whole package (site design with e commerce functionality).

I am looking to just go from scratch build my site how I see fit using my own web designing tools without having to go through a company that will give me templates to choose from. Paypal seems like the only option but there is a mothly fee for the service that allows to pay for multiple items in one shot. Pay Pals basic shopping cart which is based on a percent of the items sale (2.9% + .30) can only pay for one item at a time.

Can someone point me in the right direction for an experienced web designer new to ecommerce (I am trying to be cost effective as well since it is a very small business just starting out).

Thank you,