Hi Cool Buys -
First of all let me offer my congratulations for having done your homework before jumping in, and for spending some time working on your future!
Ebay is great in some ways - a lot of traffic, demand etc - but the fees are indeed high.
Amazon charges a final value fee that includes your processing of credit cards, and then yes by all means have your own website.
A trick to saving money on marketing your website is to build one good page. It doesn't need to be fancy but it does need to be solid and relevant to your items. Submit that page to DMOZ when you know your site will be ready in about 4-6 weeks. Every time you work on your page be sure your keywords etc are updated. I did this and had top 10 placement in google and yahoo for my business in less than 3 months without spending a ton of money.
Other than that, write down your immediate, short, and long term goals, write your road map for how you plan get to each one, be willing to learn and be flexible, and don't have a narrow vision of the markets - oh, and avoid the temptation to borrow money or use a credit card or buy stuff 'because you are a business'.
Last word of advice is that any money that comes in - divide part for your savings, part for the business, and then your pay.
Great job so far! I hope this helps spur ideas -