What an exciting opportunnity! And what a great validation of the startup process which teaches to be prepared for the unexpected and be flexible enough to respond to the market's demands.
I would consider your core business in the context of the business inquiried. What are you selling? Where are the margins? Where is the long term growth potential?
Know thy business
Being in the business of earning transactional revenue on a marketplace is a different business that developing and customizing a SaaS solution for Fortune 100 businesses. While these two options are certinally not mutually exclusive,
Understand the Cost
In pricing the development of a "white label solution" is absolutly critical that the total true costs to your company are understood. These cost include the direct programming and design cost of course. They may also include dedicated hosting with Sarbanes–Oxley complient processes or specific data security compliance requirements. there may be significant integration costs that will be hard to estimate until knowledge of either their systems are known. It might be as easy as --
The sales cost are also different. the sales cycle of closing a Fortune 100 company is often signficantly longer than a small to mid-size vendor.
Often you will know the totatlity of these costs -- it is more likly that you will not, and will need some type of discovery process to discern them.
Choice to Charge
After you know the cost you can make a strategic choice -- based on your own business capacity to carry certin costs -- to charge up front or not. there may be an advantage in your sales process of limiting the downstroke as much as possible and embedding it in the monthly or the ongoing costs. You may want to choose to provide the options to the customer based on what you learn about their purchasing culture.
*Sales Commission *
The proposed model of charging them a percentage of sales generated through the affiliate code on the co-branded site is a solid approach. Especially if it works in the targeted industry you are working. In this model your fee would be included as part of the overall sales and marketing expense incurred by the company. The amount needs to fit their own business model. In some industries the value of a qualified lead can be as high as 40%, in others the value of the closed deal can't go above 20%, in low margin industries this may be seen as way too much or the commission is paid off a line item rather than gross revenue (like net for example)
In my experience, most of the white labeled option of products/services that I have worked on have made the strategic decision to keep their business model on the ongoing service and to pass on only the costs (with standard consulting fee market-up) associated with the deployment of a white labeled solution to the new customer.
Occassionally the costs associated with customization/deployment would be negotiated to be integrated into the ongoing service fees in exchange for a longer agreement with a clear "buy-out" exit that ensure the cost of the customization/deployment would be covered by the margin in the implementation of the agreement.
Work with the first couple white labeled customers. Position yourself in the consultative sale role that is interested in develop a win-0win for them. Have them co-develop the proposal for pricing/deployment with you by providing you the information you need to meet their specific needs.
Draft out a specifi pricing sheet that includes a downstroker of X and then an ongoing service fee of X% of sales. Try to match it off another product or service that the targeted prospective customer would have been purchasing. Present it as a "starting point" and make it clear that you are looking forward to discussing with them their unique needs so that you can put together a propsoal which will make sense for their business.
Assume the sale -- not of a product -- but of a partnership.