Okay I have figured this out through some trial and error.
For those interested in a solution that does not involve having to write and install Custom Actions into the GAC. This simplest way to handle this situation is to utilize the Quest List view web part for displaying data in the list and then using the Quest List form web part (Upload option) By default SharePoint uses the Upload form located in the _layouts folder on the server this is why you need to do what states above. There is no way to force it to use the Upload form in the Forms folder of that library.
First let me note that I was unaware that the Upload form option of the Quest List Form web part was a 2 part form. The first part of the form is similar to the standard SharePoint Upload page. The second part is the custom form that you would configure. This second part gives personnel the option to Check In the document. Which is what I was looking for. This is separate from the Edit form that the document library uses. So, just like any other list you will need to configure 3 forms (Display, Edit, Upload) for custom forms.
Next if you wish to use this new upload form as the entry form for new documents you MUST use the Quest List View web part as the primary data viewer for that library. This web part by default selects the Upload form, or whatever form you have designated in SP Designer, in the Forms folder of the library you are working with.
For those of you who wish to retain the functionality of the default SharePoint list, but enable the options (custom upload form) of the Quest List view toolbar, you can edit the default SP list view to remove the toolbar and add in a Quest List view web part that displays no data and just gives you the toolbar. This is also helpful to simplify things for users, if you have multiple web parts displaying different filtered data of the same library, by giving them only ONE toolbar but multiple web part displays underneath.