You are selling into a B2B market. One of the oldest and most tested models of B2B sales is through affiliates. The advantage for your start-up is that you get to leverage the experience, connections and relationships of your affiliates to come to market.
The decision to build and leverage an affiliate network to support your sales need not be an "either/or" scenario. Be sure to build the systems to support source tracking, associated marketing support and sales support. With solid systems in these areas you will be able to support multiple go-to-market strategies.
When a company chooses an affiliate strategy they enter a duel sales effort. The first is their own product. the second is the business opportunity of selling their product. You will need the core-value-proposition for each sale. Each sale will need the appropriate materials. You will need to know and understand the psychology of the affiliates in your chosen market, as well as you understand the pain and needs of the decision maker of the medium-large eCommerce site.
Good luck with the start-up of your sales and marketing efforts!