You need to make sure that these checkboxes, when created on the client side with Javascript, have a name attribute assigned so that they are submitted in the Request.
For example:
<input type="checkbox" id="mycheck" name="mycheck" />
When the form is submitted, you can access the checkbox by looking at the request params as so:
//will probably say "on" or "checked", not sure.
string mycheckbox= HttpContext.Current.Request.Params["mycheck"];
Note that you will only see in the request parameters, the checkboxes that are checked off. If you create 5 checkboxes and only one is checked off, only the one checked off will be present in the Params collection