Don't do it.
If there were actually a prospect of the site making any real money (thus commissions being worthwhile) the guy wouldn't be offering to pay you in commissions. He's offering this payment structure because he knows the return on commissions will be far less than any standard fees you may want. In general, those offering this type of structure don't have enough faith in their own business model to pay for your services up front. If they did, they'd realize in an instant that paying any fees you have directly would be more cost effective than giving up commissions. TO be fair, many would-be entrepreneurs may also see the commission structure as "Hey! I won't have to pay him/her anything until I start making money." It may not be a malicious offer, however it's generally not a good offer unless the site/project is already making money and there are already figures for what your commissions would be in place.
If he insists upon a commission structure you need to alter it to ensure you get paid enough to compensate you at least a little. A flat fee per month plus commissions. But even then only do that if you really want to do the project. It may be better to lower the initial project fees and supplement that with commissions. For example... standard project fee minus 30%, then 5% royalty on all sales.
Working solely on commission creates an unstable client relationship in my experience. If the site makes no money, you make no money. What if the client wants you to spend 60 hours changing the site in order to increase sales? You'll be doing all that for free. What if the site merely trickles in sales and your commissions are less than $50 a month? Are you going to feel it's worth spending time to improve the design in order to increase your commissions? Realize that this may be a "hobby" for the owner, a simple secondary income venture, while in most cases it may be your primary job or source of income. So your needs may be much greater than your clients. He may be okay if the site goes 6 months without making a dime. Would you be?
If you really want to get into commission-based payments for a business site you should be treating the site as any investor would. Because, make no mistake, he's asking you to be an investor in the business. Not in terms of venture capital or direct money input, but investment in terms of your time and work. However, that's still an investment position.
What's the business plan?
What's the anticipated user base?
What's the cost of user acquisition?
What are the monitization methods?
What's the rate of user decay?
What are the projected sales for the first month? quarter? year?
What type of products is the site selling?
What's the current market demand for those products?
How are sales for the current (ebay) system?
How much time, each month, is anticipated to be needed on your part?
How long can you expect to wait before you recover your costs?
Do you like the business?
Is it something you want to be involved in?
Are you willing to work without payment in order to try and improve your returns?
Most web designers/developers get approached with "partnership" or commission structures regularly. These ventures do not pay well 99.9% of the time. If you think you've got the something in that .1 percentile, go for it. But be aware the odds of you getting paid even your base rates are stacked against you.
As for "knowing he's paying you the right amount".... as an investor (because that's what you would be) you should have the right to view sales for any given period and those amounts. Put that in a contract. If he's unwilling to do that, then don't walk, run away from his offer.