Regretfully I don't have any background experience or knowledge with Freeway (I come from RapidWeaver land).
From looking at the Mal's E-commerce website, it looks like they host the shopping cart / checkout. You add the products on the Mal's E-commerce website and then they give you the 'add to cart / 'buy now' button code to put on your website? So I visualise the system being similar to the buttons you generate with PayPal.
So one potential option would be to use a WebYep Loop to create the list of products. Inside each loop enclosure, add a Rich Text element for the product title / description / picture and then a WebYep Markup element for the button code?
I recently encountered a similar situation when building the new Time Control stack for WebYep 2. I wanted to give site authors the ability to enter a date/time range, for when some WebYep editable content should be shown. Using Short Text elements provided a good space for an author to enter the time range, and I was able to use some if(webyep_bIsEditMode() conditional logic to hide these fields on the public-facing website. I found a way of getting the contents of Short Text elements and being able to reuse it as PHP variables.
Potentially something similar could be done for a Mal's E-commerce setup - i.e. fields in edit mode to collect the product PID / button code, and hide this code to user not logged into the website.
If it is of any help, I can try signing up for a free Mal's E-commerce account at the weekend and see if we can get something working in WebYep.