Plugin can't "talk" properly to uploads

I was wondering if someone could point me in the right direction for this. I’ve written a plugin that will allow the blog manager to upload videos – just like you would within a post. The idea is that the manager would write a post (a new custom post type), upload a video (right now, it’s an swf file) copy the URL to the video and pop it into a custom field.

The idea is that the plugin then looks at the content of the custom field, and then uses code to pull out the video and play it on the back-end of the site (not the front end) through an swf player file.

However, it doesn’t work, not unless I manually upload the videos to a folder *outside* of the uploads folder, AND I have to place the “player” embed script outside of the plugins/uploads directories. Everything works as it’s supposed to, but I’d rather keep the video uploads within the uploads directory, and my “player” script within my plugins folder. There’s some permissions issue (I suspect) that doesn’t allow the item within the uploads folder to interact with the script.

Would anyone know what I should be looking for to address this? I’ve already tried looking at my logs, and they show nothing. I’d love some pointers on how to get the plugin and the uploads directory to play nice together.