If you want the conversion tracking to be simple as it was when you were marketing others' products and services, just do it the same way -- promote a single item per site. What I mean is, you experience of "simple affilite tracking" was simple because you made it so, not because affiliate tracking is any easier (if anything, it is more difficult, because of the uncertainty factor introduced when your traffic leaves your site and goes to the offer page, at which point your tracking data is limited to whatever the merchant will give you.)
You can track your traffic and conversion data by any number of different metrics. Tracking by individual product is the key data, both in terms of raw sales and sales. You should definitely track on individual products, since tracking overall web traffic to net sales is useless -- you need to know what specifically is selling on your site, and once you know that, you need to figure out why (by duplicating the sales page and experimenting with different factors, to see what increases sales, what decreases sales and what has no effect at all.) To be honest, you should have been doing this in affiliate marketing as well -- it's called "split testing" or "Link hidden: Login to view" and can dramatically increase your bottom line.
So, short version (too late!) is, in answer to your question you should track per item, not overall, for conversion. If your site is any good you'll get all kinds of non-buyer traffic that was never going to buy from you in the first place, but came in on a link to a review or an image search or whatever. But to really be successful and have meaningful data, you need to be consistently testing out your traffic to see if you can up conversion.