How do I ask a question within the checkout flow?

It is possible - and quite simple to add your own custom questions. 

Here is the technical instructions - you add any <input> or <select> tag to your form post (within the <form> tags), give it a "name" attribute and then the result will be available when you review the order in your ezimerchant admin console. 

For example - 

<select name="How did you hear about us?">

   <option value="">Please select...</option>

   <option value="google" {if OrderProperties.[How did you hear about us?] = "google"}selected="selected"{/if}>Google</option>

   <option value="yahoo" {if OrderProperties.[How did you hear about us?] = "yahoo"}selected="selected"{/if}>Yahoo</option>

   <option value="friend" {if OrderProperties.[How did you hear about us?] = "friend"}selected="selected"{/if}>Friend</option>

</select>

As you can see to repopulate the value, you use curly brace syntax {if}{/if}. This is optional, but makes for a better user experience. 

You can access the value submitted from "OrderProperties.[fieldname]", so if you then want to display the result of this form on the checkout completion page, you could output it like this:

{OrderProperties.[How did you hear about us?]}

Again, that's optional though because you will be able to see what option they selected in the ezimerchant admin console. (http://secure.ezimerchant.com/)

Or you can call ezimerchant for help.